Query psy16685
Match_columns 99
No_of_seqs 124 out of 1052
Neff 10.7
Searched_HMMs 46136
Date Fri Aug 16 19:21:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16685.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16685hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 8.4E-26 1.8E-30 134.7 1.3 89 1-91 177-265 (279)
2 KOG2462|consensus 99.8 1.3E-20 2.9E-25 112.7 2.4 95 1-97 146-243 (279)
3 KOG3576|consensus 99.6 1.2E-16 2.6E-21 92.5 -0.1 87 11-97 115-201 (267)
4 KOG3623|consensus 99.6 3.3E-16 7.2E-21 104.1 1.8 81 10-90 891-971 (1007)
5 KOG3576|consensus 99.5 5.8E-16 1.3E-20 89.7 -0.5 92 1-92 133-235 (267)
6 KOG3623|consensus 99.5 1E-14 2.2E-19 97.2 1.3 62 1-62 910-971 (1007)
7 PHA02768 hypothetical protein; 99.2 5.5E-12 1.2E-16 59.1 2.1 44 13-58 5-48 (55)
8 KOG1074|consensus 99.2 1.2E-12 2.7E-17 88.4 -0.4 65 1-65 621-692 (958)
9 KOG3608|consensus 99.2 5.6E-12 1.2E-16 78.6 1.0 93 1-93 195-316 (467)
10 PHA00733 hypothetical protein 99.2 4.3E-11 9.2E-16 66.0 3.5 81 11-93 38-123 (128)
11 KOG1074|consensus 99.1 2.5E-11 5.4E-16 82.3 2.2 61 13-73 879-939 (958)
12 PF13465 zf-H2C2_2: Zinc-finge 99.1 2.6E-11 5.6E-16 49.1 -0.0 24 1-24 2-25 (26)
13 PHA00733 hypothetical protein 99.0 8.7E-11 1.9E-15 64.8 0.1 61 3-66 64-124 (128)
14 KOG3608|consensus 98.9 6.1E-10 1.3E-14 69.7 2.2 94 1-95 279-378 (467)
15 PF13465 zf-H2C2_2: Zinc-finge 98.9 1.5E-09 3.2E-14 43.8 2.2 26 28-53 1-26 (26)
16 PHA02768 hypothetical protein; 98.9 1.3E-09 2.9E-14 51.1 2.0 42 41-84 5-46 (55)
17 PLN03086 PRLI-interacting fact 98.8 4.7E-09 1E-13 69.8 3.7 63 12-77 477-549 (567)
18 PHA00616 hypothetical protein 98.7 5.4E-09 1.2E-13 46.8 1.0 33 13-45 1-33 (44)
19 PHA00616 hypothetical protein 98.7 4.9E-09 1.1E-13 47.0 0.8 34 41-74 1-34 (44)
20 PHA00732 hypothetical protein 98.6 3.6E-08 7.8E-13 50.0 3.0 46 13-64 1-47 (79)
21 PLN03086 PRLI-interacting fact 98.5 1.3E-07 2.8E-12 63.2 4.5 68 8-80 448-515 (567)
22 KOG3993|consensus 98.3 2.7E-07 5.8E-12 59.3 1.9 53 13-65 295-380 (500)
23 PF00096 zf-C2H2: Zinc finger, 98.2 5.7E-07 1.2E-11 35.0 1.3 22 42-63 1-22 (23)
24 PF05605 zf-Di19: Drought indu 98.1 8.8E-06 1.9E-10 38.4 4.0 50 13-65 2-53 (54)
25 PF00096 zf-C2H2: Zinc finger, 98.1 2.1E-06 4.6E-11 33.3 1.4 23 14-36 1-23 (23)
26 PF13894 zf-C2H2_4: C2H2-type 98.0 5.8E-06 1.2E-10 32.1 1.6 23 42-64 1-23 (24)
27 PF13912 zf-C2H2_6: C2H2-type 97.9 4.6E-06 1E-10 33.6 1.1 24 41-64 1-24 (27)
28 PF09237 GAGA: GAGA factor; I 97.9 1.1E-05 2.4E-10 37.1 2.0 34 37-70 20-53 (54)
29 COG5189 SFP1 Putative transcri 97.9 6.3E-06 1.4E-10 51.5 1.4 52 11-62 347-419 (423)
30 PF13912 zf-C2H2_6: C2H2-type 97.8 1.4E-05 3.1E-10 32.1 1.5 25 13-37 1-25 (27)
31 PHA00732 hypothetical protein 97.7 2E-05 4.4E-10 40.0 1.8 37 41-80 1-38 (79)
32 PF13894 zf-C2H2_4: C2H2-type 97.7 3.5E-05 7.5E-10 29.8 1.9 23 14-36 1-23 (24)
33 PF12756 zf-C2H2_2: C2H2 type 97.6 4.8E-05 1E-09 39.8 2.0 51 15-65 1-74 (100)
34 PF09237 GAGA: GAGA factor; I 97.6 8.7E-05 1.9E-09 34.2 2.3 34 8-41 19-52 (54)
35 PRK04860 hypothetical protein; 97.4 0.0001 2.2E-09 42.3 2.2 35 41-79 119-153 (160)
36 smart00355 ZnF_C2H2 zinc finge 97.4 0.0001 2.2E-09 28.8 1.5 21 43-63 2-22 (26)
37 smart00355 ZnF_C2H2 zinc finge 97.2 0.00034 7.4E-09 27.2 2.0 24 14-37 1-24 (26)
38 KOG3993|consensus 97.0 0.00012 2.7E-09 47.5 -0.8 53 13-65 267-319 (500)
39 PF13909 zf-H2C2_5: C2H2-type 96.9 0.00056 1.2E-08 26.6 1.2 23 42-65 1-23 (24)
40 PF12874 zf-met: Zinc-finger o 96.7 0.00095 2.1E-08 26.1 1.2 20 15-34 2-21 (25)
41 PF12874 zf-met: Zinc-finger o 96.7 0.00081 1.8E-08 26.3 0.8 22 42-63 1-22 (25)
42 PRK04860 hypothetical protein; 96.6 0.0016 3.4E-08 37.5 1.9 39 12-54 118-156 (160)
43 PF12171 zf-C2H2_jaz: Zinc-fin 96.4 0.0018 3.8E-08 25.9 1.0 22 14-35 2-23 (27)
44 COG5189 SFP1 Putative transcri 95.9 0.0064 1.4E-07 38.6 2.0 48 39-86 347-415 (423)
45 PF05605 zf-Di19: Drought indu 95.8 0.0078 1.7E-07 28.2 1.8 47 41-90 2-50 (54)
46 PF13913 zf-C2HC_2: zinc-finge 95.8 0.0061 1.3E-07 24.0 1.2 18 43-61 4-21 (25)
47 cd00350 rubredoxin_like Rubred 95.2 0.012 2.5E-07 24.8 1.1 24 14-49 2-25 (33)
48 COG5048 FOG: Zn-finger [Genera 95.0 0.0089 1.9E-07 38.6 0.7 65 12-76 288-358 (467)
49 smart00451 ZnF_U1 U1-like zinc 95.0 0.032 6.9E-07 23.4 2.2 22 13-34 3-24 (35)
50 KOG2893|consensus 93.8 0.024 5.2E-07 34.7 0.6 41 16-60 13-53 (341)
51 PF09986 DUF2225: Uncharacteri 93.2 0.022 4.9E-07 34.3 -0.2 44 11-54 3-61 (214)
52 KOG1146|consensus 93.0 0.075 1.6E-06 39.7 2.1 55 8-62 460-539 (1406)
53 PF12756 zf-C2H2_2: C2H2 type 92.9 0.11 2.3E-06 26.9 2.2 25 13-37 50-74 (100)
54 PF09538 FYDLN_acid: Protein o 92.5 0.094 2E-06 28.3 1.6 30 14-54 10-39 (108)
55 smart00659 RPOLCX RNA polymera 92.1 0.15 3.2E-06 23.0 1.7 29 13-52 2-30 (44)
56 COG2888 Predicted Zn-ribbon RN 91.6 0.14 3E-06 24.5 1.4 9 40-48 49-57 (61)
57 PF13719 zinc_ribbon_5: zinc-r 91.2 0.23 5E-06 21.3 1.8 34 14-52 3-36 (37)
58 COG1592 Rubrerythrin [Energy p 90.6 0.2 4.3E-06 29.1 1.7 23 13-48 134-156 (166)
59 KOG2186|consensus 90.6 0.3 6.6E-06 30.2 2.5 46 14-62 4-49 (276)
60 cd00729 rubredoxin_SM Rubredox 90.5 0.16 3.5E-06 21.5 1.0 25 13-49 2-26 (34)
61 PRK00464 nrdR transcriptional 90.0 0.083 1.8E-06 30.3 -0.2 17 41-57 28-44 (154)
62 COG1997 RPL43A Ribosomal prote 89.9 0.2 4.3E-06 25.9 1.2 30 13-52 35-64 (89)
63 PF10571 UPF0547: Uncharacteri 89.6 0.21 4.5E-06 19.8 0.9 10 43-52 16-25 (26)
64 PF13717 zinc_ribbon_4: zinc-r 89.5 0.48 1E-05 20.2 2.1 33 14-51 3-35 (36)
65 PF03604 DNA_RNApol_7kD: DNA d 89.0 0.18 4E-06 21.0 0.6 28 14-52 1-28 (32)
66 COG4049 Uncharacterized protei 89.0 0.15 3.3E-06 24.0 0.3 26 37-62 13-38 (65)
67 PHA00626 hypothetical protein 89.0 0.14 3.1E-06 24.1 0.2 35 15-54 2-36 (59)
68 TIGR02098 MJ0042_CXXC MJ0042 f 89.0 0.41 8.9E-06 20.4 1.7 34 14-52 3-36 (38)
69 TIGR02300 FYDLN_acid conserved 88.3 0.37 8.1E-06 26.7 1.6 33 14-57 10-42 (129)
70 PRK00398 rpoP DNA-directed RNA 87.7 0.36 7.8E-06 21.7 1.2 30 13-52 3-32 (46)
71 TIGR00373 conserved hypothetic 87.6 0.34 7.3E-06 27.9 1.2 15 14-28 110-124 (158)
72 smart00834 CxxC_CXXC_SSSS Puta 87.5 0.12 2.6E-06 22.4 -0.5 29 14-49 6-34 (41)
73 COG5048 FOG: Zn-finger [Genera 87.2 0.28 6.1E-06 31.7 0.8 45 1-45 305-355 (467)
74 TIGR02605 CxxC_CxxC_SSSS putat 87.1 0.14 3.1E-06 23.6 -0.4 29 14-49 6-34 (52)
75 COG1996 RPC10 DNA-directed RNA 86.8 0.5 1.1E-05 21.8 1.3 30 12-51 5-34 (49)
76 PRK06266 transcription initiat 86.5 0.36 7.7E-06 28.4 1.0 29 13-50 117-145 (178)
77 KOG2893|consensus 86.2 0.38 8.2E-06 29.7 1.0 48 39-91 9-56 (341)
78 PRK14890 putative Zn-ribbon RN 85.7 0.93 2E-05 21.7 2.0 9 40-48 47-55 (59)
79 smart00531 TFIIE Transcription 85.4 0.76 1.7E-05 26.1 1.9 35 13-51 99-133 (147)
80 PF04959 ARS2: Arsenite-resist 84.5 0.61 1.3E-05 28.3 1.3 30 9-38 73-102 (214)
81 PF14353 CpXC: CpXC protein 83.9 0.12 2.6E-06 28.5 -1.8 21 40-60 37-57 (128)
82 PRK09678 DNA-binding transcrip 81.9 0.48 1E-05 23.7 0.2 42 14-57 2-45 (72)
83 KOG4173|consensus 80.4 0.46 9.9E-06 28.7 -0.3 49 15-63 108-168 (253)
84 PTZ00255 60S ribosomal protein 79.9 0.86 1.9E-05 23.8 0.7 30 13-52 36-65 (90)
85 PF12013 DUF3505: Protein of u 79.6 1.4 3.1E-05 23.5 1.5 25 42-66 81-109 (109)
86 TIGR00280 L37a ribosomal prote 77.3 0.93 2E-05 23.7 0.3 30 13-52 35-64 (91)
87 COG3357 Predicted transcriptio 77.1 1.1 2.5E-05 23.3 0.6 11 13-23 58-68 (97)
88 COG3364 Zn-ribbon containing p 76.5 2 4.2E-05 23.0 1.4 15 13-27 2-16 (112)
89 PF01780 Ribosomal_L37ae: Ribo 75.7 0.75 1.6E-05 24.0 -0.3 30 13-52 35-64 (90)
90 smart00734 ZnF_Rad18 Rad18-lik 75.4 2.1 4.6E-05 16.8 1.1 18 43-61 3-20 (26)
91 smart00614 ZnF_BED BED zinc fi 75.4 2.9 6.2E-05 19.0 1.7 21 42-62 19-44 (50)
92 PF13451 zf-trcl: Probable zin 74.6 2.3 5E-05 19.6 1.2 37 12-48 3-40 (49)
93 PF05443 ROS_MUCR: ROS/MUCR tr 74.1 2.3 5.1E-05 23.8 1.4 26 41-69 72-97 (132)
94 PF02892 zf-BED: BED zinc fing 73.8 3.4 7.4E-05 18.1 1.7 14 12-25 15-28 (45)
95 KOG2231|consensus 73.1 2.3 4.9E-05 30.2 1.4 30 42-75 183-212 (669)
96 PF04959 ARS2: Arsenite-resist 73.1 1.3 2.9E-05 26.9 0.3 27 39-65 75-101 (214)
97 PRK03976 rpl37ae 50S ribosomal 73.0 1.3 2.7E-05 23.2 0.2 30 13-52 36-65 (90)
98 PF08274 PhnA_Zn_Ribbon: PhnA 72.1 1.8 3.9E-05 17.8 0.5 24 15-49 4-27 (30)
99 PRK03824 hypA hydrogenase nick 71.4 1.7 3.6E-05 24.4 0.4 14 13-26 70-83 (135)
100 PF07754 DUF1610: Domain of un 71.4 2.1 4.5E-05 16.6 0.6 10 40-49 15-24 (24)
101 KOG2482|consensus 71.0 3.4 7.3E-05 27.1 1.7 29 42-70 196-226 (423)
102 COG1571 Predicted DNA-binding 70.2 3.3 7.2E-05 27.8 1.7 32 14-56 351-382 (421)
103 PF05191 ADK_lid: Adenylate ki 69.5 1.8 3.9E-05 18.5 0.2 9 15-23 3-11 (36)
104 KOG4167|consensus 69.4 1 2.3E-05 32.2 -0.8 25 41-65 792-816 (907)
105 PF15269 zf-C2H2_7: Zinc-finge 69.4 3.1 6.7E-05 18.8 1.0 22 42-63 21-42 (54)
106 COG4530 Uncharacterized protei 68.8 2.1 4.5E-05 23.2 0.4 28 15-53 11-38 (129)
107 KOG2785|consensus 67.5 9.9 0.00022 25.3 3.3 53 12-64 165-243 (390)
108 COG3091 SprT Zn-dependent meta 67.3 4.1 8.8E-05 23.5 1.4 34 40-78 116-149 (156)
109 smart00661 RPOL9 RNA polymeras 67.2 5.8 0.00013 17.9 1.8 32 15-54 2-33 (52)
110 KOG3507|consensus 66.9 4.3 9.3E-05 19.4 1.2 29 13-52 20-48 (62)
111 smart00440 ZnF_C2C2 C2C2 Zinc 66.6 0.89 1.9E-05 19.9 -1.0 11 41-51 28-38 (40)
112 PF07282 OrfB_Zn_ribbon: Putat 66.3 5.4 0.00012 19.3 1.6 14 39-52 44-57 (69)
113 PRK00432 30S ribosomal protein 66.0 3.8 8.2E-05 18.9 1.0 12 40-51 36-47 (50)
114 PF13453 zf-TFIIB: Transcripti 65.9 3.7 7.9E-05 17.8 0.9 21 39-59 17-37 (41)
115 KOG2593|consensus 65.8 7 0.00015 26.4 2.4 42 39-83 126-167 (436)
116 TIGR00100 hypA hydrogenase nic 65.5 2.9 6.4E-05 22.8 0.6 11 14-24 71-81 (115)
117 TIGR01206 lysW lysine biosynth 65.3 2.6 5.7E-05 19.8 0.3 31 14-52 3-33 (54)
118 PLN02294 cytochrome c oxidase 65.2 3.6 7.8E-05 24.1 1.0 15 11-25 139-153 (174)
119 PF09723 Zn-ribbon_8: Zinc rib 64.4 3.2 7E-05 18.2 0.5 29 42-77 6-34 (42)
120 KOG3408|consensus 64.4 4.7 0.0001 22.3 1.3 23 12-34 56-78 (129)
121 PF10013 DUF2256: Uncharacteri 63.9 4.8 0.0001 17.9 1.0 12 15-26 10-21 (42)
122 COG4888 Uncharacterized Zn rib 63.7 2.3 4.9E-05 22.7 -0.0 40 11-54 20-59 (104)
123 PF13878 zf-C2H2_3: zinc-finge 63.7 5.7 0.00012 17.4 1.3 23 42-64 14-38 (41)
124 COG4957 Predicted transcriptio 63.6 4 8.8E-05 23.0 0.9 25 14-41 77-101 (148)
125 COG3677 Transposase and inacti 62.0 2.6 5.7E-05 23.5 0.0 35 15-54 32-66 (129)
126 KOG2593|consensus 60.3 6.5 0.00014 26.5 1.6 40 8-50 123-162 (436)
127 PF13240 zinc_ribbon_2: zinc-r 60.2 4.4 9.5E-05 15.4 0.5 6 44-49 16-21 (23)
128 PRK12380 hydrogenase nickel in 59.9 4.5 9.9E-05 22.0 0.7 10 14-23 71-80 (113)
129 PF09845 DUF2072: Zn-ribbon co 59.8 5.3 0.00011 22.4 1.0 15 13-27 1-15 (131)
130 PF02176 zf-TRAF: TRAF-type zi 59.7 6.6 0.00014 18.3 1.2 39 12-51 8-52 (60)
131 PF04810 zf-Sec23_Sec24: Sec23 59.4 7.3 0.00016 16.9 1.2 32 13-50 2-33 (40)
132 KOG1146|consensus 59.0 3.8 8.2E-05 31.5 0.4 52 11-63 1282-1350(1406)
133 KOG2907|consensus 58.1 8.6 0.00019 21.0 1.5 12 42-53 103-114 (116)
134 KOG0978|consensus 57.2 4.5 9.7E-05 29.0 0.5 22 39-60 676-697 (698)
135 TIGR00622 ssl1 transcription f 57.1 11 0.00025 20.5 1.9 19 13-31 15-33 (112)
136 COG0068 HypF Hydrogenase matur 57.0 2.8 6.1E-05 30.0 -0.5 57 16-79 126-183 (750)
137 COG1327 Predicted transcriptio 56.7 3.1 6.8E-05 23.9 -0.2 15 41-55 28-42 (156)
138 PRK00564 hypA hydrogenase nick 56.5 5.6 0.00012 21.7 0.7 11 14-24 72-82 (117)
139 PF03811 Zn_Tnp_IS1: InsA N-te 55.9 3.6 7.7E-05 17.6 -0.1 30 14-47 6-35 (36)
140 PF11672 DUF3268: Protein of u 55.3 7.3 0.00016 20.9 1.0 37 12-49 1-39 (102)
141 KOG4167|consensus 54.5 2 4.3E-05 30.9 -1.5 26 12-37 791-816 (907)
142 COG1326 Uncharacterized archae 54.4 18 0.0004 21.8 2.6 35 13-51 6-40 (201)
143 smart00154 ZnF_AN1 AN1-like Zi 53.6 6.5 0.00014 17.0 0.6 15 13-27 12-26 (39)
144 COG2331 Uncharacterized protei 53.5 3.5 7.5E-05 20.9 -0.4 31 13-50 12-42 (82)
145 PF01428 zf-AN1: AN1-like Zinc 53.2 5.5 0.00012 17.5 0.3 15 40-54 12-26 (43)
146 TIGR00686 phnA alkylphosphonat 51.3 10 0.00022 20.6 1.1 29 15-54 4-32 (109)
147 PRK03681 hypA hydrogenase nick 51.2 8.5 0.00018 20.9 0.9 10 14-23 71-80 (114)
148 COG1655 Uncharacterized protei 50.4 4.5 9.8E-05 25.0 -0.3 40 11-50 17-71 (267)
149 KOG2807|consensus 50.4 26 0.00057 23.0 3.0 18 13-30 290-307 (378)
150 smart00731 SprT SprT homologue 50.3 13 0.00028 21.0 1.6 11 41-51 112-122 (146)
151 PF10263 SprT-like: SprT-like 50.1 6.8 0.00015 22.1 0.4 10 42-51 124-133 (157)
152 KOG2071|consensus 49.8 9.7 0.00021 26.8 1.2 28 39-66 416-443 (579)
153 PRK10220 hypothetical protein; 49.4 14 0.0003 20.1 1.5 29 15-54 5-33 (111)
154 PF14446 Prok-RING_1: Prokaryo 49.2 17 0.00037 17.1 1.6 26 14-51 6-31 (54)
155 PF10276 zf-CHCC: Zinc-finger 48.2 9 0.0002 16.8 0.6 12 40-51 28-39 (40)
156 PF01155 HypA: Hydrogenase exp 48.1 6.1 0.00013 21.4 0.0 11 14-24 71-81 (113)
157 PF04423 Rad50_zn_hook: Rad50 46.6 6.9 0.00015 18.1 0.1 13 15-27 22-34 (54)
158 PHA02998 RNA polymerase subuni 46.4 4.8 0.0001 23.9 -0.6 38 13-54 143-184 (195)
159 PF08790 zf-LYAR: LYAR-type C2 46.3 3.5 7.5E-05 16.6 -0.8 8 16-23 3-10 (28)
160 KOG1842|consensus 46.2 8.4 0.00018 26.2 0.4 26 40-65 14-39 (505)
161 PF12760 Zn_Tnp_IS1595: Transp 45.6 6.2 0.00014 17.6 -0.1 9 40-48 36-44 (46)
162 KOG2636|consensus 45.2 18 0.00039 24.7 1.8 26 8-33 396-422 (497)
163 PF14311 DUF4379: Domain of un 45.0 19 0.00041 16.6 1.5 13 42-54 29-41 (55)
164 PTZ00043 cytochrome c oxidase 44.9 11 0.00023 23.4 0.7 16 10-25 178-193 (268)
165 COG1198 PriA Primosomal protei 44.6 15 0.00032 26.8 1.4 11 40-50 474-484 (730)
166 COG1773 Rubredoxin [Energy pro 44.4 10 0.00022 17.9 0.5 15 13-27 3-17 (55)
167 PRK05452 anaerobic nitric oxid 43.7 7.4 0.00016 26.6 -0.1 16 11-26 423-438 (479)
168 PF04780 DUF629: Protein of un 43.6 17 0.00037 25.0 1.6 27 40-66 56-83 (466)
169 PF07295 DUF1451: Protein of u 43.6 10 0.00022 21.7 0.5 29 12-50 111-139 (146)
170 TIGR00627 tfb4 transcription f 43.3 21 0.00046 22.8 1.9 11 42-52 256-266 (279)
171 TIGR00416 sms DNA repair prote 43.1 19 0.0004 24.6 1.7 23 13-49 7-29 (454)
172 PF01096 TFIIS_C: Transcriptio 42.5 0.76 1.6E-05 20.0 -3.3 10 42-51 29-38 (39)
173 PF14803 Nudix_N_2: Nudix N-te 42.0 6.1 0.00013 16.6 -0.4 11 40-50 21-31 (34)
174 PRK11823 DNA repair protein Ra 41.7 19 0.00042 24.4 1.6 24 12-49 6-29 (446)
175 PRK04351 hypothetical protein; 41.6 17 0.00038 20.8 1.2 31 41-79 112-142 (149)
176 PF08209 Sgf11: Sgf11 (transcr 41.5 31 0.00068 14.4 1.7 22 41-63 4-25 (33)
177 PRK12496 hypothetical protein; 41.1 15 0.00033 21.3 1.0 11 42-52 128-138 (164)
178 COG0675 Transposase and inacti 40.8 18 0.00039 22.9 1.3 16 39-54 320-335 (364)
179 PRK14892 putative transcriptio 40.7 13 0.00027 19.9 0.5 35 12-53 20-54 (99)
180 KOG0717|consensus 40.5 16 0.00036 25.1 1.1 22 42-63 293-314 (508)
181 PF01215 COX5B: Cytochrome c o 40.3 9.1 0.0002 21.7 -0.1 14 12-25 111-124 (136)
182 PF07975 C1_4: TFIIH C1-like d 40.2 10 0.00022 17.6 0.1 23 12-34 20-42 (51)
183 COG4391 Uncharacterized protei 38.9 10 0.00022 18.3 0.0 45 4-52 15-59 (62)
184 PF01927 Mut7-C: Mut7-C RNAse 38.7 29 0.00062 19.7 1.8 46 14-59 92-142 (147)
185 PRK00762 hypA hydrogenase nick 38.6 15 0.00033 20.3 0.7 10 14-24 71-80 (124)
186 TIGR00595 priA primosomal prot 38.4 21 0.00046 24.7 1.4 10 40-49 252-261 (505)
187 PF01363 FYVE: FYVE zinc finge 38.2 22 0.00048 17.0 1.2 28 14-53 10-37 (69)
188 COG1998 RPS31 Ribosomal protei 37.0 24 0.00052 16.3 1.1 10 41-50 37-46 (51)
189 PRK06260 threonine synthase; V 36.4 24 0.00053 23.5 1.5 27 14-52 4-30 (397)
190 PRK14873 primosome assembly pr 36.1 24 0.00051 25.5 1.4 10 40-49 421-430 (665)
191 PF06397 Desulfoferrod_N: Desu 35.4 18 0.00039 15.5 0.5 12 12-23 5-16 (36)
192 PRK05978 hypothetical protein; 34.7 23 0.00049 20.4 1.0 10 43-52 54-63 (148)
193 KOG1280|consensus 34.7 44 0.00096 22.2 2.3 37 12-48 78-116 (381)
194 smart00064 FYVE Protein presen 34.6 30 0.00064 16.5 1.3 28 14-53 11-38 (68)
195 KOG1088|consensus 33.7 22 0.00049 19.6 0.8 20 8-27 93-112 (124)
196 cd00730 rubredoxin Rubredoxin; 33.3 17 0.00037 16.7 0.3 13 42-54 2-14 (50)
197 PF04606 Ogr_Delta: Ogr/Delta- 33.0 8.9 0.00019 17.2 -0.7 38 15-54 1-40 (47)
198 PF05180 zf-DNL: DNL zinc fing 32.9 2.9 6.3E-05 20.5 -2.4 42 13-57 4-45 (66)
199 COG1579 Zn-ribbon protein, pos 32.5 33 0.00071 21.5 1.5 32 15-50 199-230 (239)
200 PF00130 C1_1: Phorbol esters/ 32.1 44 0.00094 15.0 1.6 30 11-51 9-38 (53)
201 COG1675 TFA1 Transcription ini 32.0 29 0.00063 20.6 1.2 8 42-49 133-140 (176)
202 PF00301 Rubredoxin: Rubredoxi 32.0 19 0.00041 16.4 0.3 36 14-50 2-43 (47)
203 PF07800 DUF1644: Protein of u 31.9 55 0.0012 19.2 2.2 56 13-70 80-138 (162)
204 PLN03238 probable histone acet 31.8 49 0.0011 21.3 2.2 27 39-65 46-72 (290)
205 cd00924 Cyt_c_Oxidase_Vb Cytoc 31.7 24 0.00052 18.7 0.7 20 33-53 72-91 (97)
206 PF10537 WAC_Acf1_DNA_bd: ATP- 31.5 90 0.002 16.7 3.0 38 12-50 2-39 (102)
207 cd01121 Sms Sms (bacterial rad 30.9 32 0.00068 22.9 1.3 9 14-22 1-9 (372)
208 PTZ00448 hypothetical protein; 30.7 31 0.00067 23.0 1.2 23 41-63 314-336 (373)
209 KOG2857|consensus 30.2 24 0.00052 20.2 0.6 23 40-62 16-38 (157)
210 PF08792 A2L_zn_ribbon: A2L zi 30.1 27 0.00058 14.5 0.6 12 13-24 21-32 (33)
211 COG5109 Uncharacterized conser 30.1 37 0.00081 22.3 1.4 42 9-53 347-388 (396)
212 COG1779 C4-type Zn-finger prot 30.0 13 0.00029 22.4 -0.4 40 13-54 14-56 (201)
213 PHA02942 putative transposase; 29.9 36 0.00079 22.7 1.5 14 39-52 340-353 (383)
214 KOG0696|consensus 29.9 26 0.00056 24.2 0.8 58 11-77 71-129 (683)
215 PF12773 DZR: Double zinc ribb 29.7 39 0.00085 15.0 1.2 11 40-50 28-38 (50)
216 COG5236 Uncharacterized conser 29.6 30 0.00065 23.0 1.0 33 43-76 222-254 (493)
217 PF11789 zf-Nse: Zinc-finger o 29.6 36 0.00077 16.0 1.0 16 40-55 23-38 (57)
218 COG5112 UFD2 U1-like Zn-finger 29.5 22 0.00048 19.3 0.4 23 12-34 54-76 (126)
219 KOG3362|consensus 28.5 14 0.00031 21.1 -0.5 22 41-62 129-150 (156)
220 COG1594 RPB9 DNA-directed RNA 28.0 16 0.00035 19.9 -0.3 11 42-52 101-111 (113)
221 KOG1813|consensus 28.0 40 0.00086 21.9 1.3 15 40-54 240-254 (313)
222 PF05207 zf-CSL: CSL zinc fing 27.2 28 0.0006 16.3 0.4 31 13-49 18-48 (55)
223 KOG2231|consensus 26.9 73 0.0016 23.2 2.5 47 15-65 184-236 (669)
224 COG5152 Uncharacterized conser 26.5 32 0.0007 20.9 0.7 15 40-54 195-209 (259)
225 COG5188 PRP9 Splicing factor 3 26.5 51 0.0011 22.1 1.6 26 8-33 369-395 (470)
226 PF14369 zf-RING_3: zinc-finge 26.2 32 0.0007 14.4 0.5 10 15-24 23-32 (35)
227 PF09963 DUF2197: Uncharacteri 26.0 44 0.00095 15.9 1.0 37 14-51 3-41 (56)
228 PRK04023 DNA polymerase II lar 25.9 74 0.0016 24.5 2.4 9 14-22 627-635 (1121)
229 PF12907 zf-met2: Zinc-binding 25.9 25 0.00055 15.4 0.2 20 43-62 3-25 (40)
230 KOG3352|consensus 25.9 30 0.00066 20.0 0.5 13 12-24 132-144 (153)
231 COG4896 Uncharacterized protei 25.6 62 0.0013 15.7 1.4 40 14-53 3-43 (68)
232 TIGR00515 accD acetyl-CoA carb 25.6 45 0.00097 21.4 1.3 31 14-53 27-57 (285)
233 PRK06450 threonine synthase; V 25.5 54 0.0012 21.4 1.7 26 14-52 4-29 (338)
234 PF13824 zf-Mss51: Zinc-finger 25.5 48 0.001 15.7 1.1 13 11-23 12-24 (55)
235 PLN02748 tRNA dimethylallyltra 25.4 63 0.0014 22.4 2.0 24 12-35 417-441 (468)
236 PF10071 DUF2310: Zn-ribbon-co 25.4 35 0.00076 21.6 0.7 27 15-48 222-248 (258)
237 PRK07591 threonine synthase; V 25.2 48 0.001 22.4 1.4 28 13-53 18-45 (421)
238 PRK08222 hydrogenase 4 subunit 24.6 62 0.0013 19.1 1.6 19 12-30 113-131 (181)
239 PF02891 zf-MIZ: MIZ/SP-RING z 24.3 29 0.00064 15.8 0.2 10 40-49 40-49 (50)
240 COG1379 PHP family phosphoeste 24.2 30 0.00064 22.9 0.3 12 41-52 265-276 (403)
241 PF01286 XPA_N: XPA protein N- 24.2 33 0.00072 14.4 0.4 13 14-26 4-16 (34)
242 KOG0402|consensus 24.2 23 0.0005 18.3 -0.2 12 40-51 53-64 (92)
243 PRK05580 primosome assembly pr 24.1 52 0.0011 23.8 1.5 11 40-50 420-430 (679)
244 CHL00174 accD acetyl-CoA carbo 24.1 25 0.00054 22.7 -0.0 32 14-54 39-70 (296)
245 COG1066 Sms Predicted ATP-depe 24.1 47 0.001 22.8 1.2 13 12-24 6-18 (456)
246 PF12230 PRP21_like_P: Pre-mRN 24.0 26 0.00056 21.4 0.0 31 40-71 167-197 (229)
247 KOG4727|consensus 24.0 49 0.0011 19.7 1.1 22 13-34 75-96 (193)
248 TIGR00244 transcriptional regu 23.7 38 0.00082 19.5 0.6 17 13-29 28-44 (147)
249 TIGR00319 desulf_FeS4 desulfof 23.7 40 0.00086 13.8 0.6 12 12-23 6-17 (34)
250 PLN00104 MYST -like histone ac 23.7 59 0.0013 22.4 1.6 25 40-64 197-221 (450)
251 PRK12722 transcriptional activ 23.5 54 0.0012 19.7 1.2 32 40-79 133-164 (187)
252 PRK00420 hypothetical protein; 23.3 61 0.0013 17.8 1.3 13 41-53 40-52 (112)
253 PF14205 Cys_rich_KTR: Cystein 23.3 36 0.00078 16.1 0.4 10 13-22 4-13 (55)
254 PRK12860 transcriptional activ 23.0 54 0.0012 19.8 1.2 49 23-80 117-165 (189)
255 KOG1994|consensus 23.0 66 0.0014 20.1 1.5 21 40-60 238-258 (268)
256 PF05741 zf-nanos: Nanos RNA b 22.9 30 0.00064 16.4 0.1 11 12-22 32-42 (55)
257 COG4338 Uncharacterized protei 22.8 25 0.00054 16.1 -0.2 11 43-53 14-24 (54)
258 cd00974 DSRD Desulforedoxin (D 22.7 42 0.00092 13.7 0.5 11 13-23 4-14 (34)
259 PF14690 zf-ISL3: zinc-finger 22.6 50 0.0011 14.3 0.8 10 13-22 2-11 (47)
260 TIGR03831 YgiT_finger YgiT-typ 22.5 40 0.00087 14.4 0.5 14 40-53 31-44 (46)
261 TIGR01384 TFS_arch transcripti 22.5 15 0.00032 19.4 -1.1 8 42-49 63-70 (104)
262 PF02318 FYVE_2: FYVE-type zin 22.5 49 0.0011 18.0 0.9 12 13-24 54-65 (118)
263 PF14255 Cys_rich_CPXG: Cystei 22.1 36 0.00077 15.9 0.3 10 43-52 2-11 (52)
264 TIGR01385 TFSII transcription 22.0 24 0.00053 22.7 -0.4 10 42-51 287-296 (299)
265 smart00647 IBR In Between Ring 22.0 55 0.0012 15.0 0.9 17 38-54 37-53 (64)
266 COG5151 SSL1 RNA polymerase II 21.9 38 0.00083 22.2 0.5 24 41-64 388-411 (421)
267 COG0846 SIR2 NAD-dependent pro 21.7 62 0.0013 20.4 1.3 38 8-49 117-154 (250)
268 PF06524 NOA36: NOA36 protein; 21.7 21 0.00046 22.7 -0.7 18 40-57 208-225 (314)
269 PF14787 zf-CCHC_5: GAG-polypr 21.7 54 0.0012 14.0 0.8 11 15-25 4-14 (36)
270 PTZ00064 histone acetyltransfe 21.7 75 0.0016 22.4 1.8 25 40-64 279-303 (552)
271 cd01410 SIRT7 SIRT7: Eukaryoti 21.6 1.2E+02 0.0026 18.3 2.5 39 8-49 90-128 (206)
272 PF11023 DUF2614: Protein of u 21.2 74 0.0016 17.5 1.4 10 13-22 69-78 (114)
273 PF08271 TF_Zn_Ribbon: TFIIB z 20.9 57 0.0012 14.1 0.8 29 14-51 1-29 (43)
274 PF06170 DUF983: Protein of un 20.8 47 0.001 17.2 0.6 12 43-54 10-21 (86)
275 PF06220 zf-U1: U1 zinc finger 20.7 94 0.002 13.2 1.5 12 13-24 3-14 (38)
276 PF09297 zf-NADH-PPase: NADH p 20.6 42 0.00091 13.5 0.3 11 39-49 19-29 (32)
277 COG2051 RPS27A Ribosomal prote 20.2 46 0.00099 16.4 0.4 14 40-53 37-50 (67)
278 PRK05654 acetyl-CoA carboxylas 20.1 32 0.0007 22.1 -0.1 31 14-53 28-58 (292)
279 PRK00415 rps27e 30S ribosomal 20.1 66 0.0014 15.5 1.0 15 40-54 29-43 (59)
No 1
>KOG2462|consensus
Probab=99.91 E-value=8.4e-26 Score=134.73 Aligned_cols=89 Identities=33% Similarity=0.456 Sum_probs=83.5
Q ss_pred CeehhhhhcCCCCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchHHHHHHhccCCCcchhhhcccccc
Q psy16685 1 MIYILRVLISEKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNLEPV 80 (99)
Q Consensus 1 l~~h~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~ 80 (99)
|.+|+|+|+ -|+.|.+||+.|..+..|+.|+++|+|+|||.|+.|+++|...++|+.|+++|.++|+|.|..|+..+.
T Consensus 177 LkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFs 254 (279)
T KOG2462|consen 177 LKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFA 254 (279)
T ss_pred HhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHH
Confidence 578999988 488999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCCcchhhhhh
Q psy16685 81 SGSNDEKNLNK 91 (99)
Q Consensus 81 ~~~~~~~~~~~ 91 (99)
.-+.+++|...
T Consensus 255 l~SyLnKH~ES 265 (279)
T KOG2462|consen 255 LKSYLNKHSES 265 (279)
T ss_pred HHHHHHHhhhh
Confidence 88888888754
No 2
>KOG2462|consensus
Probab=99.80 E-value=1.3e-20 Score=112.66 Aligned_cols=95 Identities=24% Similarity=0.291 Sum_probs=85.9
Q ss_pred CeehhhhhcC---CCCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchHHHHHHhccCCCcchhhhccc
Q psy16685 1 MIYILRVLIS---EKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNL 77 (99)
Q Consensus 1 l~~h~~~h~~---~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~ 77 (99)
|.+|+.+|-. .+.+.|..|++.|.+-..|+.|+++|+ -+.+|..||+.|.++.-|+.|+|+|+|||||.|..|+.
T Consensus 146 LsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~k 223 (279)
T KOG2462|consen 146 LSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGK 223 (279)
T ss_pred cchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccc
Confidence 5677777653 466889999999999999999999987 57999999999999999999999999999999999999
Q ss_pred cccCCCcchhhhhhhhhhhc
Q psy16685 78 EPVSGSNDEKNLNKFNIVKA 97 (99)
Q Consensus 78 ~~~~~~~~~~~~~~~~~~~~ 97 (99)
.+.+.+++..||.+...++.
T Consensus 224 AFADRSNLRAHmQTHS~~K~ 243 (279)
T KOG2462|consen 224 AFADRSNLRAHMQTHSDVKK 243 (279)
T ss_pred hhcchHHHHHHHHhhcCCcc
Confidence 99999999999999887664
No 3
>KOG3576|consensus
Probab=99.59 E-value=1.2e-16 Score=92.53 Aligned_cols=87 Identities=30% Similarity=0.436 Sum_probs=67.6
Q ss_pred CCCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchHHHHHHhccCCCcchhhhccccccCCCcchhhhh
Q psy16685 11 EKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNLEPVSGSNDEKNLN 90 (99)
Q Consensus 11 ~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (99)
...+.|.+|++.|...-.|.+|++.|...+.+.|..||+.|...-.|++|+++|+|.+||.|..|...+...-.++.|+.
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHH
Confidence 34577888888887777777888888777778888888888877778888888888888888888888877777788877
Q ss_pred hhhhhhc
Q psy16685 91 KFNIVKA 97 (99)
Q Consensus 91 ~~~~~~~ 97 (99)
+++.+..
T Consensus 195 kvhgv~~ 201 (267)
T KOG3576|consen 195 KVHGVQH 201 (267)
T ss_pred HHcCchH
Confidence 7776543
No 4
>KOG3623|consensus
Probab=99.59 E-value=3.3e-16 Score=104.12 Aligned_cols=81 Identities=26% Similarity=0.404 Sum_probs=71.3
Q ss_pred CCCCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchHHHHHHhccCCCcchhhhccccccCCCcchhhh
Q psy16685 10 SEKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNLEPVSGSNDEKNL 89 (99)
Q Consensus 10 ~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (99)
...+|.|++|.++|...+.|.+|..-|+|.+||+|.+|.++|..+-.|..|+|+|.|||||.|.+|+..+.-...-..||
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 34589999999999999999999999999999999999999999999999999999999999999998876655555555
Q ss_pred h
Q psy16685 90 N 90 (99)
Q Consensus 90 ~ 90 (99)
+
T Consensus 971 N 971 (1007)
T KOG3623|consen 971 N 971 (1007)
T ss_pred c
Confidence 4
No 5
>KOG3576|consensus
Probab=99.54 E-value=5.8e-16 Score=89.72 Aligned_cols=92 Identities=25% Similarity=0.378 Sum_probs=79.1
Q ss_pred CeehhhhhcCCCCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchHHHHHHhcc-----------CCCc
Q psy16685 1 MIYILRVLISEKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYHRMTHI-----------KVND 69 (99)
Q Consensus 1 l~~h~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~-----------~~~~ 69 (99)
|.+|+..|...+.|.|..||+.|...-.|++|+++|+|.+||+|..|+++|.....|..|.+.-+ .++-
T Consensus 133 lnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl 212 (267)
T KOG3576|consen 133 LNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKL 212 (267)
T ss_pred HHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhhe
Confidence 57899999999999999999999999999999999999999999999999999999999987433 3677
Q ss_pred chhhhccccccCCCcchhhhhhh
Q psy16685 70 DFKEILNLEPVSGSNDEKNLNKF 92 (99)
Q Consensus 70 ~~~~~~~~~~~~~~~~~~~~~~~ 92 (99)
|.|+-|+...........|+...
T Consensus 213 ~vcedcg~t~~~~e~~~~h~~~~ 235 (267)
T KOG3576|consen 213 YVCEDCGYTSERPEVYYLHLKLH 235 (267)
T ss_pred eeecccCCCCCChhHHHHHHHhc
Confidence 88899988776666555555433
No 6
>KOG3623|consensus
Probab=99.47 E-value=1e-14 Score=97.20 Aligned_cols=62 Identities=35% Similarity=0.643 Sum_probs=59.6
Q ss_pred CeehhhhhcCCCCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchHHHHHH
Q psy16685 1 MIYILRVLISEKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYHRM 62 (99)
Q Consensus 1 l~~h~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 62 (99)
|.||.=-|+|.+||.|.+|.+.|..+..|..|.+.|.|++||+|..|++.|.....+..||.
T Consensus 910 LaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 910 LARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred HHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 56888889999999999999999999999999999999999999999999999999999988
No 7
>PHA02768 hypothetical protein; Provisional
Probab=99.23 E-value=5.5e-12 Score=59.08 Aligned_cols=44 Identities=18% Similarity=0.324 Sum_probs=38.3
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchHH
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLY 58 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~ 58 (99)
-|.|+.||+.|.....|..|+++|+ ++++|..|++.|.+.+.|.
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 4789999999999999999999988 6889999999998877664
No 8
>KOG1074|consensus
Probab=99.22 E-value=1.2e-12 Score=88.38 Aligned_cols=65 Identities=28% Similarity=0.641 Sum_probs=51.2
Q ss_pred CeehhhhhcCCCCeecccCcCcCCChHHHHHHhhhcCCCC----ceecc---cccccccCcchHHHHHHhcc
Q psy16685 1 MIYILRVLISEKPHVCSVCSKGFSTSSSLNTHRRIHSGEK----PHQCQ---VCGKRFTASSNLYYHRMTHI 65 (99)
Q Consensus 1 l~~h~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~----~~~C~---~C~~~f~~~~~l~~H~~~h~ 65 (99)
|+.|.|+|+|++||+|.+||+.|.++.+|+.|+.+|.... .+.|+ +|.+.|...-.|..|.++|.
T Consensus 621 LqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lpQhIriH~ 692 (958)
T KOG1074|consen 621 LQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLPQHIRIHL 692 (958)
T ss_pred hhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccccceEEeec
Confidence 5678888888888888888888888888888888776543 35677 78888888888888888876
No 9
>KOG3608|consensus
Probab=99.18 E-value=5.6e-12 Score=78.60 Aligned_cols=93 Identities=22% Similarity=0.256 Sum_probs=73.8
Q ss_pred CeehhhhhcCCCCeecccCcCcCCChHHHHHHhhhcCC--CCc--------------------------eeccccccccc
Q psy16685 1 MIYILRVLISEKPHVCSVCSKGFSTSSSLNTHRRIHSG--EKP--------------------------HQCQVCGKRFT 52 (99)
Q Consensus 1 l~~h~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~--~~~--------------------------~~C~~C~~~f~ 52 (99)
|.+|.|.|++++...|+.||..|.+++.|..|.+..+. ..+ |+|+.|+.+..
T Consensus 195 LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~ 274 (467)
T KOG3608|consen 195 LREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCS 274 (467)
T ss_pred HHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCC
Confidence 56899999999999999999999999888888765433 123 56777777777
Q ss_pred CcchHHHHHHh-ccCCCcchhhhccccccCCCcchhhhhhhh
Q psy16685 53 ASSNLYYHRMT-HIKVNDDFKEILNLEPVSGSNDEKNLNKFN 93 (99)
Q Consensus 53 ~~~~l~~H~~~-h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 93 (99)
..+.|..|++. |...+|+.|.-|.......+++.+|.+..+
T Consensus 275 ~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 275 SASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred ChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 77778888774 678899999999988888888888887554
No 10
>PHA00733 hypothetical protein
Probab=99.15 E-value=4.3e-11 Score=66.04 Aligned_cols=81 Identities=15% Similarity=0.128 Sum_probs=49.7
Q ss_pred CCCeecccCcCcCCChHHHHHH--hh---hcCCCCceecccccccccCcchHHHHHHhccCCCcchhhhccccccCCCcc
Q psy16685 11 EKPHVCSVCSKGFSTSSSLNTH--RR---IHSGEKPHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNLEPVSGSND 85 (99)
Q Consensus 11 ~~~~~C~~c~~~~~~~~~l~~h--~~---~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~ 85 (99)
.+++.|.+|...|..+..+..+ +. ...+.+||.|+.|++.|.....|..|++.+ +.++.|..|+..+.....+
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHH
Confidence 3456677776666665544433 11 122356777777777777777777777655 3456777777777666666
Q ss_pred hhhhhhhh
Q psy16685 86 EKNLNKFN 93 (99)
Q Consensus 86 ~~~~~~~~ 93 (99)
..|+.+.+
T Consensus 116 ~~H~~~~h 123 (128)
T PHA00733 116 LDHVCKKH 123 (128)
T ss_pred HHHHHHhc
Confidence 66665544
No 11
>KOG1074|consensus
Probab=99.12 E-value=2.5e-11 Score=82.27 Aligned_cols=61 Identities=43% Similarity=0.762 Sum_probs=57.6
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchHHHHHHhccCCCcchhh
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKE 73 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~ 73 (99)
...|..|++.|.....|+.|+++|++.+||.|..|++.|....+|+.||.+|+|..+..-.
T Consensus 879 ~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srr 939 (958)
T KOG1074|consen 879 AHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRR 939 (958)
T ss_pred hhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCccC
Confidence 4679999999999999999999999999999999999999999999999999998887655
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=99.05 E-value=2.6e-11 Score=49.07 Aligned_cols=24 Identities=38% Similarity=0.664 Sum_probs=16.6
Q ss_pred CeehhhhhcCCCCeecccCcCcCC
Q psy16685 1 MIYILRVLISEKPHVCSVCSKGFS 24 (99)
Q Consensus 1 l~~h~~~h~~~~~~~C~~c~~~~~ 24 (99)
|.+|+++|++++||.|+.|++.|.
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 456777777777777777776664
No 13
>PHA00733 hypothetical protein
Probab=98.98 E-value=8.7e-11 Score=64.81 Aligned_cols=61 Identities=33% Similarity=0.567 Sum_probs=51.5
Q ss_pred ehhhhhcCCCCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchHHHHHHhccC
Q psy16685 3 YILRVLISEKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYHRMTHIK 66 (99)
Q Consensus 3 ~h~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 66 (99)
+|+.+ .+.+||.|+.|++.|.....|..|++.+ ..++.|..|++.|.....|..|+...++
T Consensus 64 ~~~~~-~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 64 KLLTS-KAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred hhccc-CCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 34333 4588999999999999999999999876 3579999999999999999999886553
No 14
>KOG3608|consensus
Probab=98.92 E-value=6.1e-10 Score=69.72 Aligned_cols=94 Identities=19% Similarity=0.191 Sum_probs=71.1
Q ss_pred Ceehhhh-hcCCCCeecccCcCcCCChHHHHHHhhhcCCCCceeccc--ccccccCcchHHHHHHhcc-C--CCcchhhh
Q psy16685 1 MIYILRV-LISEKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQV--CGKRFTASSNLYYHRMTHI-K--VNDDFKEI 74 (99)
Q Consensus 1 l~~h~~~-h~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~-~--~~~~~~~~ 74 (99)
|.+|++. |...+|++|+.|...+...+.|..|..+|. ...|.|.. |...|.....+.+|++-++ | +-+|.|..
T Consensus 279 L~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~ 357 (467)
T KOG3608|consen 279 LTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHC 357 (467)
T ss_pred HHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeec
Confidence 3456665 667788888888888888888888877776 45678865 8888888888888877543 3 46788888
Q ss_pred ccccccCCCcchhhhhhhhhh
Q psy16685 75 LNLEPVSGSNDEKNLNKFNIV 95 (99)
Q Consensus 75 ~~~~~~~~~~~~~~~~~~~~~ 95 (99)
|...+.++.++..|+.+.+..
T Consensus 358 Cdr~ft~G~~L~~HL~kkH~f 378 (467)
T KOG3608|consen 358 CDRFFTSGKSLSAHLMKKHGF 378 (467)
T ss_pred chhhhccchhHHHHHHHhhcc
Confidence 888888888888888877643
No 15
>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=98.89 E-value=1.5e-09 Score=43.83 Aligned_cols=26 Identities=50% Similarity=1.034 Sum_probs=22.1
Q ss_pred HHHHHhhhcCCCCceecccccccccC
Q psy16685 28 SLNTHRRIHSGEKPHQCQVCGKRFTA 53 (99)
Q Consensus 28 ~l~~h~~~~~~~~~~~C~~C~~~f~~ 53 (99)
+|..|+++|++++||.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 46789999999999999999988853
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.87 E-value=1.3e-09 Score=51.08 Aligned_cols=42 Identities=12% Similarity=0.216 Sum_probs=36.8
Q ss_pred ceecccccccccCcchHHHHHHhccCCCcchhhhccccccCCCc
Q psy16685 41 PHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNLEPVSGSN 84 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~ 84 (99)
.|+|+.||+.|...++|..|+++|+ +++.|..|+..+...+.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~ 46 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGE 46 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccce
Confidence 4899999999999999999999999 68899999987765544
No 17
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.81 E-value=4.7e-09 Score=69.77 Aligned_cols=63 Identities=14% Similarity=0.249 Sum_probs=29.7
Q ss_pred CCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccC----------cchHHHHHHhccCCCcchhhhccc
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTA----------SSNLYYHRMTHIKVNDDFKEILNL 77 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~----------~~~l~~H~~~h~~~~~~~~~~~~~ 77 (99)
.|+.|+ ||..+ ....|..|+.++...+++.|..|+..|.. ...|..|.... +.++..|..|+.
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk 549 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGR 549 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCC
Confidence 345555 55332 33445555555555555555555554421 12445554442 455555555543
No 18
>PHA00616 hypothetical protein
Probab=98.70 E-value=5.4e-09 Score=46.84 Aligned_cols=33 Identities=12% Similarity=0.108 Sum_probs=20.9
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceecc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQ 45 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~ 45 (99)
||.|..||+.|.....+..|++.+++.+++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 456666666666666666666666666666554
No 19
>PHA00616 hypothetical protein
Probab=98.70 E-value=4.9e-09 Score=46.99 Aligned_cols=34 Identities=26% Similarity=0.305 Sum_probs=31.3
Q ss_pred ceecccccccccCcchHHHHHHhccCCCcchhhh
Q psy16685 41 PHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEI 74 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~ 74 (99)
||+|+.||+.|...+.+..|++.|++++++.+..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999988653
No 20
>PHA00732 hypothetical protein
Probab=98.63 E-value=3.6e-08 Score=50.04 Aligned_cols=46 Identities=28% Similarity=0.535 Sum_probs=38.0
Q ss_pred CeecccCcCcCCChHHHHHHhhh-cCCCCceecccccccccCcchHHHHHHhc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRI-HSGEKPHQCQVCGKRFTASSNLYYHRMTH 64 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~-~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 64 (99)
||.|..|++.|.....|..|++. |. ++.|+.|++.|. .+..|....
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhccc
Confidence 68899999999999999999884 54 358999999997 467776543
No 21
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.55 E-value=1.3e-07 Score=63.15 Aligned_cols=68 Identities=15% Similarity=0.310 Sum_probs=57.3
Q ss_pred hcCCCCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchHHHHHHhccCCCcchhhhcccccc
Q psy16685 8 LISEKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNLEPV 80 (99)
Q Consensus 8 h~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~ 80 (99)
...++.+.|..|+..|. ...+..|...++ +++.|+ |+..+ ....|..|+.+|...++..|..|+....
T Consensus 448 ~el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 448 EEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQ 515 (567)
T ss_pred cccccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccc
Confidence 34456678999999996 577899999874 789999 99765 6689999999999999999999998764
No 22
>KOG3993|consensus
Probab=98.33 E-value=2.7e-07 Score=59.26 Aligned_cols=53 Identities=36% Similarity=0.679 Sum_probs=46.5
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCC--------C-------------------------CceecccccccccCcchHHH
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSG--------E-------------------------KPHQCQVCGKRFTASSNLYY 59 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~--------~-------------------------~~~~C~~C~~~f~~~~~l~~ 59 (99)
-|.|++|+++|.-..+|..|.++|.- . ..|.|..|++.|.+...|+.
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrK 374 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRK 374 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHH
Confidence 58999999999999999999999832 1 13889999999999999999
Q ss_pred HHHhcc
Q psy16685 60 HRMTHI 65 (99)
Q Consensus 60 H~~~h~ 65 (99)
|+.+|.
T Consensus 375 Hqlthq 380 (500)
T KOG3993|consen 375 HQLTHQ 380 (500)
T ss_pred hHHhhh
Confidence 988876
No 23
>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=98.25 E-value=5.7e-07 Score=34.98 Aligned_cols=22 Identities=41% Similarity=0.803 Sum_probs=13.2
Q ss_pred eecccccccccCcchHHHHHHh
Q psy16685 42 HQCQVCGKRFTASSNLYYHRMT 63 (99)
Q Consensus 42 ~~C~~C~~~f~~~~~l~~H~~~ 63 (99)
|.|+.|++.|.+...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4566666666666666666554
No 24
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.10 E-value=8.8e-06 Score=38.37 Aligned_cols=50 Identities=32% Similarity=0.489 Sum_probs=38.0
Q ss_pred CeecccCcCcCCChHHHHHHhhh-cCC-CCceecccccccccCcchHHHHHHhcc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRI-HSG-EKPHQCQVCGKRFTASSNLYYHRMTHI 65 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~-~~~-~~~~~C~~C~~~f~~~~~l~~H~~~h~ 65 (99)
.|.|+.|++ ..+...|..|... |.. .+.+.|+.|...+. .+|..|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 478999999 5557789999665 444 35789999998644 48999988754
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=98.08 E-value=2.1e-06 Score=33.28 Aligned_cols=23 Identities=43% Similarity=0.836 Sum_probs=20.9
Q ss_pred eecccCcCcCCChHHHHHHhhhc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIH 36 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~ 36 (99)
|.|+.|++.|..+..|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 68999999999999999998764
No 26
>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=97.95 E-value=5.8e-06 Score=32.09 Aligned_cols=23 Identities=48% Similarity=0.881 Sum_probs=12.1
Q ss_pred eecccccccccCcchHHHHHHhc
Q psy16685 42 HQCQVCGKRFTASSNLYYHRMTH 64 (99)
Q Consensus 42 ~~C~~C~~~f~~~~~l~~H~~~h 64 (99)
|.|+.|+..|.+...|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 45556666666666666665543
No 27
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.93 E-value=4.6e-06 Score=33.61 Aligned_cols=24 Identities=42% Similarity=0.891 Sum_probs=14.1
Q ss_pred ceecccccccccCcchHHHHHHhc
Q psy16685 41 PHQCQVCGKRFTASSNLYYHRMTH 64 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~h 64 (99)
||.|..|+..|.+...|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 355666666666666666665544
No 28
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.89 E-value=1.1e-05 Score=37.09 Aligned_cols=34 Identities=26% Similarity=0.434 Sum_probs=23.4
Q ss_pred CCCCceecccccccccCcchHHHHHHhccCCCcc
Q psy16685 37 SGEKPHQCQVCGKRFTASSNLYYHRMTHIKVNDD 70 (99)
Q Consensus 37 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~ 70 (99)
.++.|-.|+.|+..+.+..+|++|+++.++.+|.
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~~ 53 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKPG 53 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS--
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccCC
Confidence 3467889999999999999999999988887764
No 29
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.86 E-value=6.3e-06 Score=51.51 Aligned_cols=52 Identities=37% Similarity=0.738 Sum_probs=37.9
Q ss_pred CCCeeccc--CcCcCCChHHHHHHhhhcC-------------------CCCceecccccccccCcchHHHHHH
Q psy16685 11 EKPHVCSV--CSKGFSTSSSLNTHRRIHS-------------------GEKPHQCQVCGKRFTASSNLYYHRM 62 (99)
Q Consensus 11 ~~~~~C~~--c~~~~~~~~~l~~h~~~~~-------------------~~~~~~C~~C~~~f~~~~~l~~H~~ 62 (99)
++||.|++ |.+.++....|+-|+.--+ ..+||.|+.|++.+..-..|+.|+.
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 48888866 8888888877777754211 1368888888888888888877754
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.80 E-value=1.4e-05 Score=32.11 Aligned_cols=25 Identities=44% Similarity=0.846 Sum_probs=22.9
Q ss_pred CeecccCcCcCCChHHHHHHhhhcC
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHS 37 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~ 37 (99)
||.|..|++.|.+...|..|++.|.
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 6899999999999999999998764
No 31
>PHA00732 hypothetical protein
Probab=97.73 E-value=2e-05 Score=40.00 Aligned_cols=37 Identities=19% Similarity=0.182 Sum_probs=31.6
Q ss_pred ceecccccccccCcchHHHHHHh-ccCCCcchhhhcccccc
Q psy16685 41 PHQCQVCGKRFTASSNLYYHRMT-HIKVNDDFKEILNLEPV 80 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~~~~~~~~~~ 80 (99)
||.|..|++.|.+...|..|++. |.+ +.|..|+..+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~ 38 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR 38 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC
Confidence 68899999999999999999985 553 57888888776
No 32
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.71 E-value=3.5e-05 Score=29.76 Aligned_cols=23 Identities=39% Similarity=0.846 Sum_probs=19.2
Q ss_pred eecccCcCcCCChHHHHHHhhhc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIH 36 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~ 36 (99)
|.|+.|+..|.+...+..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 68999999999999999998875
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.59 E-value=4.8e-05 Score=39.82 Aligned_cols=51 Identities=25% Similarity=0.551 Sum_probs=21.3
Q ss_pred ecccCcCcCCChHHHHHHhhhcCC-----------------------CCceecccccccccCcchHHHHHHhcc
Q psy16685 15 VCSVCSKGFSTSSSLNTHRRIHSG-----------------------EKPHQCQVCGKRFTASSNLYYHRMTHI 65 (99)
Q Consensus 15 ~C~~c~~~~~~~~~l~~h~~~~~~-----------------------~~~~~C~~C~~~f~~~~~l~~H~~~h~ 65 (99)
+|..|+..|.....+..|+....+ ...+.|..|+..|.+...|..|++.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 367777777777777777654322 124889999999999999999999643
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=97.55 E-value=8.7e-05 Score=34.18 Aligned_cols=34 Identities=32% Similarity=0.555 Sum_probs=24.1
Q ss_pred hcCCCCeecccCcCcCCChHHHHHHhhhcCCCCc
Q psy16685 8 LISEKPHVCSVCSKGFSTSSSLNTHRRIHSGEKP 41 (99)
Q Consensus 8 h~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~ 41 (99)
+..+.|..|++|+..+.+..+|.+|+...++.+|
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 3456799999999999999999999988777665
No 35
>PRK04860 hypothetical protein; Provisional
Probab=97.45 E-value=0.0001 Score=42.31 Aligned_cols=35 Identities=11% Similarity=0.045 Sum_probs=22.5
Q ss_pred ceecccccccccCcchHHHHHHhccCCCcchhhhccccc
Q psy16685 41 PHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNLEP 79 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~ 79 (99)
+|.|. |+. ....+.+|.+++.+++++.|..|+...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCcee
Confidence 56665 665 455566777777777777777666543
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.41 E-value=0.0001 Score=28.79 Aligned_cols=21 Identities=43% Similarity=0.710 Sum_probs=10.6
Q ss_pred ecccccccccCcchHHHHHHh
Q psy16685 43 QCQVCGKRFTASSNLYYHRMT 63 (99)
Q Consensus 43 ~C~~C~~~f~~~~~l~~H~~~ 63 (99)
.|..|++.|.....|..|++.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHH
Confidence 344555555555555555443
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.22 E-value=0.00034 Score=27.20 Aligned_cols=24 Identities=38% Similarity=0.685 Sum_probs=21.1
Q ss_pred eecccCcCcCCChHHHHHHhhhcC
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHS 37 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~ 37 (99)
|.|..|++.|.....+..|+..|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999988654
No 38
>KOG3993|consensus
Probab=96.96 E-value=0.00012 Score=47.45 Aligned_cols=53 Identities=26% Similarity=0.495 Sum_probs=42.9
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchHHHHHHhcc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYHRMTHI 65 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 65 (99)
-|.|..|-..|...-.|.+|.=.-.-..-|+|+.|++.|.-..+|..|+|.|.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccC
Confidence 36799999889888888887433322345999999999999999999999874
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.92 E-value=0.00056 Score=26.56 Aligned_cols=23 Identities=30% Similarity=0.431 Sum_probs=13.4
Q ss_pred eecccccccccCcchHHHHHHhcc
Q psy16685 42 HQCQVCGKRFTASSNLYYHRMTHI 65 (99)
Q Consensus 42 ~~C~~C~~~f~~~~~l~~H~~~h~ 65 (99)
|+|+.|+.... +..|..|++.++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 46677776665 666777766543
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.74 E-value=0.00095 Score=26.07 Aligned_cols=20 Identities=45% Similarity=0.946 Sum_probs=9.6
Q ss_pred ecccCcCcCCChHHHHHHhh
Q psy16685 15 VCSVCSKGFSTSSSLNTHRR 34 (99)
Q Consensus 15 ~C~~c~~~~~~~~~l~~h~~ 34 (99)
.|..|+..|.+...+..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 34455555555544444443
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.68 E-value=0.00081 Score=26.27 Aligned_cols=22 Identities=27% Similarity=0.671 Sum_probs=19.9
Q ss_pred eecccccccccCcchHHHHHHh
Q psy16685 42 HQCQVCGKRFTASSNLYYHRMT 63 (99)
Q Consensus 42 ~~C~~C~~~f~~~~~l~~H~~~ 63 (99)
|.|..|+..|.+...+..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 6799999999999999999874
No 42
>PRK04860 hypothetical protein; Provisional
Probab=96.59 E-value=0.0016 Score=37.49 Aligned_cols=39 Identities=26% Similarity=0.640 Sum_probs=33.0
Q ss_pred CCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCc
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTAS 54 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 54 (99)
-+|.|. |+. ....+..|.+++++.++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 369998 987 566778999999999999999999887654
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=96.40 E-value=0.0018 Score=25.91 Aligned_cols=22 Identities=32% Similarity=0.668 Sum_probs=14.5
Q ss_pred eecccCcCcCCChHHHHHHhhh
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRI 35 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~ 35 (99)
|.|..|++.|.+...+..|+.+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 4577777777777766666543
No 44
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.86 E-value=0.0064 Score=38.57 Aligned_cols=48 Identities=21% Similarity=0.292 Sum_probs=37.4
Q ss_pred CCceecc--cccccccCcchHHHHHHhcc-------------------CCCcchhhhccccccCCCcch
Q psy16685 39 EKPHQCQ--VCGKRFTASSNLYYHRMTHI-------------------KVNDDFKEILNLEPVSGSNDE 86 (99)
Q Consensus 39 ~~~~~C~--~C~~~f~~~~~l~~H~~~h~-------------------~~~~~~~~~~~~~~~~~~~~~ 86 (99)
++||+|+ .|.+.+.....|+.|+.-.+ ..|||.|++|+........+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLK 415 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLK 415 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccce
Confidence 5899996 59999999999999987422 359999999987765544443
No 45
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=95.82 E-value=0.0078 Score=28.20 Aligned_cols=47 Identities=26% Similarity=0.282 Sum_probs=31.9
Q ss_pred ceecccccccccCcchHHHHHHh-ccC-CCcchhhhccccccCCCcchhhhh
Q psy16685 41 PHQCQVCGKRFTASSNLYYHRMT-HIK-VNDDFKEILNLEPVSGSNDEKNLN 90 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~-h~~-~~~~~~~~~~~~~~~~~~~~~~~~ 90 (99)
.|.|+.|++ ..+...|..|... |.. .+...|-+|..... .++..|+.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~ 50 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLN 50 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHH
Confidence 478999999 5567889999776 444 35677888876322 24444444
No 46
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.80 E-value=0.0061 Score=23.99 Aligned_cols=18 Identities=33% Similarity=0.947 Sum_probs=8.7
Q ss_pred ecccccccccCcchHHHHH
Q psy16685 43 QCQVCGKRFTASSNLYYHR 61 (99)
Q Consensus 43 ~C~~C~~~f~~~~~l~~H~ 61 (99)
.|+.||+.| ..+.|..|+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHE 21 (25)
T ss_pred cCCCCCCEE-CHHHHHHHH
Confidence 455555555 333444444
No 47
>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=95.21 E-value=0.012 Score=24.76 Aligned_cols=24 Identities=38% Similarity=0.888 Sum_probs=16.8
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccccc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGK 49 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 49 (99)
|.|..||..+.... .++.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 67888887654322 6788888875
No 48
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.03 E-value=0.0089 Score=38.58 Aligned_cols=65 Identities=38% Similarity=0.660 Sum_probs=55.7
Q ss_pred CCeecccCcCcCCChHHHHHHhh--hcCCC--Cceecc--cccccccCcchHHHHHHhccCCCcchhhhcc
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRR--IHSGE--KPHQCQ--VCGKRFTASSNLYYHRMTHIKVNDDFKEILN 76 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~ 76 (99)
.++.|..|...|.....+..|.+ .|.++ +++.|+ .|+..|.....+..|..+|.+..+..+....
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 358 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLN 358 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccccccc
Confidence 36789999999999999999999 79998 899999 7999999999999999999887766654444
No 49
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.00 E-value=0.032 Score=23.38 Aligned_cols=22 Identities=23% Similarity=0.593 Sum_probs=16.0
Q ss_pred CeecccCcCcCCChHHHHHHhh
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRR 34 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~ 34 (99)
+|.|..|+..|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5678888888877777766654
No 50
>KOG2893|consensus
Probab=93.82 E-value=0.024 Score=34.72 Aligned_cols=41 Identities=27% Similarity=0.680 Sum_probs=33.4
Q ss_pred cccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchHHHH
Q psy16685 16 CSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYH 60 (99)
Q Consensus 16 C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H 60 (99)
|..|.+.|....-|.+|++ .+.|+|-+|-+..-+-..|..|
T Consensus 13 cwycnrefddekiliqhqk----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceee
Confidence 8899999999988888766 5789999998766666667666
No 51
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=93.21 E-value=0.022 Score=34.32 Aligned_cols=44 Identities=32% Similarity=0.598 Sum_probs=28.7
Q ss_pred CCCeecccCcCcCCChHHHHHHhhh---cC-------CCCc-----eecccccccccCc
Q psy16685 11 EKPHVCSVCSKGFSTSSSLNTHRRI---HS-------GEKP-----HQCQVCGKRFTAS 54 (99)
Q Consensus 11 ~~~~~C~~c~~~~~~~~~l~~h~~~---~~-------~~~~-----~~C~~C~~~f~~~ 54 (99)
++...|+.|+..|.++.-.....+. .+ +..| +.|+.||.++...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 3567899999999987544433332 11 1222 5899999887644
No 52
>KOG1146|consensus
Probab=93.04 E-value=0.075 Score=39.68 Aligned_cols=55 Identities=25% Similarity=0.393 Sum_probs=45.3
Q ss_pred hcCCCCeecccCcCcCCChHHHHHHhhhcC-------------------------CCCceecccccccccCcchHHHHHH
Q psy16685 8 LISEKPHVCSVCSKGFSTSSSLNTHRRIHS-------------------------GEKPHQCQVCGKRFTASSNLYYHRM 62 (99)
Q Consensus 8 h~~~~~~~C~~c~~~~~~~~~l~~h~~~~~-------------------------~~~~~~C~~C~~~f~~~~~l~~H~~ 62 (99)
+.-.+.+.|+.|+..|+....|..|++..+ +.++|.|..|...+....+|.+|+.
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 344578899999999999999999988711 1247889999999999999999987
No 53
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=92.90 E-value=0.11 Score=26.89 Aligned_cols=25 Identities=28% Similarity=0.603 Sum_probs=21.7
Q ss_pred CeecccCcCcCCChHHHHHHhhhcC
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHS 37 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~ 37 (99)
.+.|..|+..|.+...|..|++.+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 6899999999999999999999753
No 54
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=92.52 E-value=0.094 Score=28.30 Aligned_cols=30 Identities=27% Similarity=0.741 Sum_probs=23.6
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTAS 54 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 54 (99)
..|+.||..|.- .+..|..|+.||..|...
T Consensus 10 R~Cp~CG~kFYD-----------Lnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD-----------LNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc-----------CCCCCccCCCCCCccCcc
Confidence 369999988854 234788999999988766
No 55
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=92.07 E-value=0.15 Score=22.95 Aligned_cols=29 Identities=21% Similarity=0.575 Sum_probs=21.0
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
.|.|..||..|... ...+..|+.||....
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~rIl 30 (44)
T smart00659 2 IYICGECGRENEIK-----------SKDVVRCRECGYRIL 30 (44)
T ss_pred EEECCCCCCEeecC-----------CCCceECCCCCceEE
Confidence 37899999877543 235789999986543
No 56
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.60 E-value=0.14 Score=24.50 Aligned_cols=9 Identities=44% Similarity=1.309 Sum_probs=4.4
Q ss_pred Cceeccccc
Q psy16685 40 KPHQCQVCG 48 (99)
Q Consensus 40 ~~~~C~~C~ 48 (99)
.+|.|+.||
T Consensus 49 ~~Y~Cp~CG 57 (61)
T COG2888 49 NPYRCPKCG 57 (61)
T ss_pred CceECCCcC
Confidence 345555554
No 57
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=91.22 E-value=0.23 Score=21.33 Aligned_cols=34 Identities=24% Similarity=0.664 Sum_probs=23.6
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
..|+.|+..|.....- ...+....+|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~-----l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-----LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH-----cccCCcEEECCCCCcEee
Confidence 4689999888766532 123445789999988774
No 58
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=90.64 E-value=0.2 Score=29.13 Aligned_cols=23 Identities=48% Similarity=1.155 Sum_probs=13.6
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceeccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCG 48 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~ 48 (99)
-|.|++||.. +.++.|..||.||
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCC
Confidence 4667777643 2345566777776
No 59
>KOG2186|consensus
Probab=90.59 E-value=0.3 Score=30.23 Aligned_cols=46 Identities=22% Similarity=0.472 Sum_probs=34.9
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchHHHHHH
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYHRM 62 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 62 (99)
|.|..||....-+ .+..|+..-.+ .-|.|.-|+..|.. ..+..|..
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 6799999877644 46678777666 67999999999988 55666655
No 60
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=90.55 E-value=0.16 Score=21.45 Aligned_cols=25 Identities=36% Similarity=0.872 Sum_probs=15.8
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceecccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGK 49 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 49 (99)
.|.|..||..+... ..|..|+.|+.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCC
Confidence 36788888654321 24668888875
No 61
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=89.99 E-value=0.083 Score=30.33 Aligned_cols=17 Identities=41% Similarity=0.921 Sum_probs=13.0
Q ss_pred ceecccccccccCcchH
Q psy16685 41 PHQCQVCGKRFTASSNL 57 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~~l 57 (99)
.++|+.||.+|.....+
T Consensus 28 ~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 28 RRECLACGKRFTTFERV 44 (154)
T ss_pred eeeccccCCcceEeEec
Confidence 48899999998876443
No 62
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=89.91 E-value=0.2 Score=25.88 Aligned_cols=30 Identities=30% Similarity=0.804 Sum_probs=19.2
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
+|.|+.|++.- ..+ .+...|.|..|+..|.
T Consensus 35 ~~~Cp~C~~~~--------VkR--~a~GIW~C~kCg~~fA 64 (89)
T COG1997 35 KHVCPFCGRTT--------VKR--IATGIWKCRKCGAKFA 64 (89)
T ss_pred CCcCCCCCCcc--------eee--eccCeEEcCCCCCeec
Confidence 57788887641 111 2345788888887765
No 63
>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=89.58 E-value=0.21 Score=19.80 Aligned_cols=10 Identities=40% Similarity=0.976 Sum_probs=7.8
Q ss_pred eccccccccc
Q psy16685 43 QCQVCGKRFT 52 (99)
Q Consensus 43 ~C~~C~~~f~ 52 (99)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 7888888774
No 64
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=89.53 E-value=0.48 Score=20.24 Aligned_cols=33 Identities=21% Similarity=0.588 Sum_probs=23.0
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccccccc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRF 51 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 51 (99)
..|+.|+..|...... +.......+|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEe
Confidence 4688999888776643 22334568899998776
No 65
>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=89.04 E-value=0.18 Score=21.03 Aligned_cols=28 Identities=25% Similarity=0.693 Sum_probs=17.4
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
|.|..|+..+..+ ...+..|+.||....
T Consensus 1 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RIl 28 (32)
T PF03604_consen 1 YICGECGAEVELK-----------PGDPIRCPECGHRIL 28 (32)
T ss_dssp EBESSSSSSE-BS-----------TSSTSSBSSSS-SEE
T ss_pred CCCCcCCCeeEcC-----------CCCcEECCcCCCeEE
Confidence 5788888766421 234678999986543
No 66
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=89.00 E-value=0.15 Score=24.04 Aligned_cols=26 Identities=27% Similarity=0.505 Sum_probs=17.2
Q ss_pred CCCCceecccccccccCcchHHHHHH
Q psy16685 37 SGEKPHQCQVCGKRFTASSNLYYHRM 62 (99)
Q Consensus 37 ~~~~~~~C~~C~~~f~~~~~l~~H~~ 62 (99)
.|+.-+.|+-|+..|.....+.+|..
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhh
Confidence 44555677777777776666666655
No 67
>PHA00626 hypothetical protein
Probab=88.99 E-value=0.14 Score=24.14 Aligned_cols=35 Identities=17% Similarity=0.363 Sum_probs=20.3
Q ss_pred ecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCc
Q psy16685 15 VCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTAS 54 (99)
Q Consensus 15 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 54 (99)
.|+.||..-..+... .......|.|..||..|...
T Consensus 2 ~CP~CGS~~Ivrcg~-----cr~~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSGNIAKEKT-----MRGWSDDYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCceeeeece-----ecccCcceEcCCCCCeechh
Confidence 478888642222111 11224679999999888543
No 68
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=88.99 E-value=0.41 Score=20.45 Aligned_cols=34 Identities=21% Similarity=0.455 Sum_probs=22.2
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
..|+.|+..|....... ......+.|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCEEECCCCCCEEE
Confidence 57999998887655321 11223578999987764
No 69
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=88.32 E-value=0.37 Score=26.71 Aligned_cols=33 Identities=18% Similarity=0.437 Sum_probs=24.5
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchH
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNL 57 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l 57 (99)
..|+.||..|.- .+..|..|+.||..|.....+
T Consensus 10 r~Cp~cg~kFYD-----------Lnk~p~vcP~cg~~~~~~~~~ 42 (129)
T TIGR02300 10 RICPNTGSKFYD-----------LNRRPAVSPYTGEQFPPEEAL 42 (129)
T ss_pred ccCCCcCccccc-----------cCCCCccCCCcCCccCcchhh
Confidence 479999988853 234789999999988665443
No 70
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.73 E-value=0.36 Score=21.69 Aligned_cols=30 Identities=20% Similarity=0.507 Sum_probs=20.3
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
.|.|+.||..+..... ...+.|+.||..+.
T Consensus 3 ~y~C~~CG~~~~~~~~----------~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEY----------GTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCC----------CCceECCCCCCeEE
Confidence 5889999987654221 12689999986543
No 71
>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=87.58 E-value=0.34 Score=27.94 Aligned_cols=15 Identities=13% Similarity=0.394 Sum_probs=7.0
Q ss_pred eecccCcCcCCChHH
Q psy16685 14 HVCSVCSKGFSTSSS 28 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~ 28 (99)
|.|+.|+..|+....
T Consensus 110 Y~Cp~c~~r~tf~eA 124 (158)
T TIGR00373 110 FICPNMCVRFTFNEA 124 (158)
T ss_pred EECCCCCcEeeHHHH
Confidence 445555544444433
No 72
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=87.50 E-value=0.12 Score=22.40 Aligned_cols=29 Identities=24% Similarity=0.597 Sum_probs=18.8
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccccc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGK 49 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 49 (99)
|.|..||..|...... .......|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~-------~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKI-------SDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEec-------CCCCCCCCCCCCC
Confidence 6799999877643321 1134567888886
No 73
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=87.16 E-value=0.28 Score=31.72 Aligned_cols=45 Identities=31% Similarity=0.530 Sum_probs=38.4
Q ss_pred Ceehhh--hhcCC--CCeecc--cCcCcCCChHHHHHHhhhcCCCCceecc
Q psy16685 1 MIYILR--VLISE--KPHVCS--VCSKGFSTSSSLNTHRRIHSGEKPHQCQ 45 (99)
Q Consensus 1 l~~h~~--~h~~~--~~~~C~--~c~~~~~~~~~l~~h~~~~~~~~~~~C~ 45 (99)
|.+|.+ .|.++ +|+.|+ .|+..|.....+..|...+.+..++.+.
T Consensus 305 l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 305 LTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred ccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 457778 79999 999999 8999999999999999999887766654
No 74
>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=87.09 E-value=0.14 Score=23.55 Aligned_cols=29 Identities=21% Similarity=0.620 Sum_probs=18.4
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccccc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGK 49 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 49 (99)
|.|..|+..|.....+ . ...+..|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~------~-~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKM------S-DDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEec------C-CCCCCCCCCCCC
Confidence 6799999877643221 1 134567888885
No 75
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=86.75 E-value=0.5 Score=21.75 Aligned_cols=30 Identities=20% Similarity=0.577 Sum_probs=20.5
Q ss_pred CCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccc
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRF 51 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 51 (99)
.-|.|..||+.|... .......|+.||...
T Consensus 5 ~~Y~C~~Cg~~~~~~----------~~~~~irCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGREVELD----------QETRGIRCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCeeehh----------hccCceeCCCCCcEE
Confidence 358899999888211 123567999998653
No 76
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=86.53 E-value=0.36 Score=28.42 Aligned_cols=29 Identities=21% Similarity=0.587 Sum_probs=14.6
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceeccccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKR 50 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 50 (99)
-|.|+.|+..|+....+. .-|.|+.||..
T Consensus 117 ~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~ 145 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAME---------YGFRCPQCGEM 145 (178)
T ss_pred EEECCCCCcEEeHHHHhh---------cCCcCCCCCCC
Confidence 355666665555444331 23566666543
No 77
>KOG2893|consensus
Probab=86.20 E-value=0.38 Score=29.69 Aligned_cols=48 Identities=21% Similarity=0.291 Sum_probs=37.4
Q ss_pred CCceecccccccccCcchHHHHHHhccCCCcchhhhccccccCCCcchhhhhh
Q psy16685 39 EKPHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNLEPVSGSNDEKNLNK 91 (99)
Q Consensus 39 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~ 91 (99)
.+|| |=.|.+.|..+..|..|++ .+-|.|.+|-.+..++-.+..|-.-
T Consensus 9 ~kpw-cwycnrefddekiliqhqk----akhfkchichkkl~sgpglsihcmq 56 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIHCMQ 56 (341)
T ss_pred CCce-eeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceeehhh
Confidence 3555 5679999999999999887 4558999999988887777665433
No 78
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=85.73 E-value=0.93 Score=21.69 Aligned_cols=9 Identities=44% Similarity=1.254 Sum_probs=4.1
Q ss_pred Cceeccccc
Q psy16685 40 KPHQCQVCG 48 (99)
Q Consensus 40 ~~~~C~~C~ 48 (99)
.+|.|+.||
T Consensus 47 ~~Y~CP~CG 55 (59)
T PRK14890 47 NPYTCPKCG 55 (59)
T ss_pred CceECCCCC
Confidence 344444444
No 79
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=85.38 E-value=0.76 Score=26.08 Aligned_cols=35 Identities=14% Similarity=0.402 Sum_probs=16.9
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceecccccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRF 51 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 51 (99)
-|.|+.|+..|.....+.. .. . ...|.|+.||...
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~-~d--~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQL-LD--M-DGTFTCPRCGEEL 133 (147)
T ss_pred EEECcCCCCEeeHHHHHHh-cC--C-CCcEECCCCCCEE
Confidence 4666666666654332211 00 1 2236666666543
No 80
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=84.45 E-value=0.61 Score=28.30 Aligned_cols=30 Identities=20% Similarity=0.283 Sum_probs=21.3
Q ss_pred cCCCCeecccCcCcCCChHHHHHHhhhcCC
Q psy16685 9 ISEKPHVCSVCSKGFSTSSSLNTHRRIHSG 38 (99)
Q Consensus 9 ~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~ 38 (99)
.++..|.|..|++.|.....+..|+...+.
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 345568899999999999988888876544
No 81
>PF14353 CpXC: CpXC protein
Probab=83.92 E-value=0.12 Score=28.54 Aligned_cols=21 Identities=33% Similarity=0.785 Sum_probs=15.6
Q ss_pred CceecccccccccCcchHHHH
Q psy16685 40 KPHQCQVCGKRFTASSNLYYH 60 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~~~l~~H 60 (99)
..+.|+.||..|.-...+..|
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred CEEECCCCCCceecCCCEEEE
Confidence 357999999988776666544
No 82
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=81.93 E-value=0.48 Score=23.67 Aligned_cols=42 Identities=24% Similarity=0.471 Sum_probs=25.3
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecc--cccccccCcchH
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQ--VCGKRFTASSNL 57 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~--~C~~~f~~~~~l 57 (99)
+.|+.||..-....+-. +.....+..+.|. .||.+|.....+
T Consensus 2 m~CP~Cg~~a~irtSr~--~s~~~~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCPLCQHAAHARTSRY--ITDTTKERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred ccCCCCCCccEEEEChh--cChhhheeeeecCCCCCCCEEEEEEEE
Confidence 46899987653332211 1112345667897 899998876544
No 83
>KOG4173|consensus
Probab=80.35 E-value=0.46 Score=28.66 Aligned_cols=49 Identities=31% Similarity=0.609 Sum_probs=38.5
Q ss_pred ecccCcCcCCChHHHHHHhhh-c---------CCCCceec--ccccccccCcchHHHHHHh
Q psy16685 15 VCSVCSKGFSTSSSLNTHRRI-H---------SGEKPHQC--QVCGKRFTASSNLYYHRMT 63 (99)
Q Consensus 15 ~C~~c~~~~~~~~~l~~h~~~-~---------~~~~~~~C--~~C~~~f~~~~~l~~H~~~ 63 (99)
.|..|.+.|++..-|..|+.- | .|..-|+| ..|+..|.+....+.|+-.
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIR 168 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHH
Confidence 699999999999988888653 3 22334788 5799999999999999764
No 84
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=79.87 E-value=0.86 Score=23.79 Aligned_cols=30 Identities=20% Similarity=0.445 Sum_probs=17.7
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
.|.|+.|++.-.. -.+...|.|..|++.|.
T Consensus 36 ~y~CpfCgk~~vk----------R~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 36 KYFCPFCGKHAVK----------RQAVGIWRCKGCKKTVA 65 (90)
T ss_pred CccCCCCCCCcee----------eeeeEEEEcCCCCCEEe
Confidence 6778888743111 11235688888877664
No 85
>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=79.62 E-value=1.4 Score=23.54 Aligned_cols=25 Identities=16% Similarity=0.274 Sum_probs=21.2
Q ss_pred eec----ccccccccCcchHHHHHHhccC
Q psy16685 42 HQC----QVCGKRFTASSNLYYHRMTHIK 66 (99)
Q Consensus 42 ~~C----~~C~~~f~~~~~l~~H~~~h~~ 66 (99)
|.| ..|+....+...+..|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 789 8899999999999999887654
No 86
>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=77.30 E-value=0.93 Score=23.72 Aligned_cols=30 Identities=27% Similarity=0.670 Sum_probs=18.1
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
.|.|+.|++.-. . -.+...|.|..|+..|.
T Consensus 35 ~y~CpfCgk~~v-----k-----R~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 35 KYVCPFCGKKTV-----K-----RGSTGIWTCRKCGAKFA 64 (91)
T ss_pred CccCCCCCCCce-----E-----EEeeEEEEcCCCCCEEe
Confidence 577888874311 1 12234688888887664
No 87
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=77.07 E-value=1.1 Score=23.33 Aligned_cols=11 Identities=36% Similarity=0.893 Sum_probs=5.2
Q ss_pred CeecccCcCcC
Q psy16685 13 PHVCSVCSKGF 23 (99)
Q Consensus 13 ~~~C~~c~~~~ 23 (99)
|..|..||..|
T Consensus 58 Pa~CkkCGfef 68 (97)
T COG3357 58 PARCKKCGFEF 68 (97)
T ss_pred ChhhcccCccc
Confidence 44444444444
No 88
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=76.55 E-value=2 Score=23.00 Aligned_cols=15 Identities=40% Similarity=0.955 Sum_probs=12.5
Q ss_pred CeecccCcCcCCChH
Q psy16685 13 PHVCSVCSKGFSTSS 27 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~ 27 (99)
|+.|..||..|..-+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 788999999998743
No 89
>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=75.70 E-value=0.75 Score=24.02 Aligned_cols=30 Identities=30% Similarity=0.706 Sum_probs=17.5
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
.|.|+.|++.-.. + .+.-.|.|..|+..|.
T Consensus 35 ky~Cp~Cgk~~vk--------R--~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTSVK--------R--VATGIWKCKKCGKKFA 64 (90)
T ss_dssp -BEESSSSSSEEE--------E--EETTEEEETTTTEEEE
T ss_pred CCcCCCCCCceeE--------E--eeeEEeecCCCCCEEe
Confidence 5778888754211 1 1234588888887664
No 90
>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=75.41 E-value=2.1 Score=16.79 Aligned_cols=18 Identities=28% Similarity=0.530 Sum_probs=9.5
Q ss_pred ecccccccccCcchHHHHH
Q psy16685 43 QCQVCGKRFTASSNLYYHR 61 (99)
Q Consensus 43 ~C~~C~~~f~~~~~l~~H~ 61 (99)
.|+.|+..+ ....+..|.
T Consensus 3 ~CPiC~~~v-~~~~in~HL 20 (26)
T smart00734 3 QCPVCFREV-PENLINSHL 20 (26)
T ss_pred cCCCCcCcc-cHHHHHHHH
Confidence 466666655 334445554
No 91
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=75.39 E-value=2.9 Score=19.04 Aligned_cols=21 Identities=43% Similarity=0.796 Sum_probs=11.7
Q ss_pred eecccccccccCc-----chHHHHHH
Q psy16685 42 HQCQVCGKRFTAS-----SNLYYHRM 62 (99)
Q Consensus 42 ~~C~~C~~~f~~~-----~~l~~H~~ 62 (99)
..|..|++.+... ++|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 3566666555433 46666666
No 92
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=74.60 E-value=2.3 Score=19.60 Aligned_cols=37 Identities=19% Similarity=0.442 Sum_probs=18.7
Q ss_pred CCeecccCcCcCCChHHHHHHhhh-cCCCCceeccccc
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRRI-HSGEKPHQCQVCG 48 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~~-~~~~~~~~C~~C~ 48 (99)
+.+.|..||..|.-...=+..-.. .....|-.|+.|-
T Consensus 3 k~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR 40 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCR 40 (49)
T ss_pred eeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHH
Confidence 456788888777644332222111 1123456666663
No 93
>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=74.06 E-value=2.3 Score=23.85 Aligned_cols=26 Identities=35% Similarity=0.533 Sum_probs=15.5
Q ss_pred ceecccccccccCcchHHHHHHhccCCCc
Q psy16685 41 PHQCQVCGKRFTASSNLYYHRMTHIKVND 69 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 69 (99)
-..|-.||+.|.. |++|.+.|+|-.|
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eeEEccCCcccch---HHHHHHHccCCCH
Confidence 4679999998754 5899999866544
No 94
>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=73.79 E-value=3.4 Score=18.10 Aligned_cols=14 Identities=29% Similarity=0.515 Sum_probs=5.6
Q ss_pred CCeecccCcCcCCC
Q psy16685 12 KPHVCSVCSKGFST 25 (99)
Q Consensus 12 ~~~~C~~c~~~~~~ 25 (99)
....|..|++.+..
T Consensus 15 ~~a~C~~C~~~~~~ 28 (45)
T PF02892_consen 15 KKAKCKYCGKVIKY 28 (45)
T ss_dssp S-EEETTTTEE---
T ss_pred CeEEeCCCCeEEee
Confidence 34456666555443
No 95
>KOG2231|consensus
Probab=73.11 E-value=2.3 Score=30.24 Aligned_cols=30 Identities=27% Similarity=0.541 Sum_probs=20.0
Q ss_pred eecccccccccCcchHHHHHHhccCCCcchhhhc
Q psy16685 42 HQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEIL 75 (99)
Q Consensus 42 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~ 75 (99)
-.|..|...|.....|.+|++.++ ++|..|
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h----~~chfC 212 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH----EFCHFC 212 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce----eheeec
Confidence 456777777777777777777555 444444
No 96
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=73.11 E-value=1.3 Score=26.91 Aligned_cols=27 Identities=26% Similarity=0.538 Sum_probs=20.9
Q ss_pred CCceecccccccccCcchHHHHHHhcc
Q psy16685 39 EKPHQCQVCGKRFTASSNLYYHRMTHI 65 (99)
Q Consensus 39 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 65 (99)
+..|.|..|++.|.-......|+...+
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcC
Confidence 346999999999999999999988755
No 97
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=73.01 E-value=1.3 Score=23.18 Aligned_cols=30 Identities=33% Similarity=0.839 Sum_probs=17.6
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
.|.|+.|++.-.. -.+...|.|..|+..|.
T Consensus 36 ~y~CpfCgk~~vk----------R~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 36 KHVCPVCGRPKVK----------RVGTGIWECRKCGAKFA 65 (90)
T ss_pred CccCCCCCCCceE----------EEEEEEEEcCCCCCEEe
Confidence 5778888643111 11234688888877664
No 98
>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=72.09 E-value=1.8 Score=17.76 Aligned_cols=24 Identities=21% Similarity=0.709 Sum_probs=11.0
Q ss_pred ecccCcCcCCChHHHHHHhhhcCCCCceecccccc
Q psy16685 15 VCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGK 49 (99)
Q Consensus 15 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 49 (99)
.|+.|+..+.. .....+.|+.|+.
T Consensus 4 ~Cp~C~se~~y-----------~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTY-----------EDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----E-----------E-SSSEEETTTTE
T ss_pred CCCCCCCccee-----------ccCCEEeCCcccc
Confidence 57888766543 3345688888875
No 99
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=71.38 E-value=1.7 Score=24.42 Aligned_cols=14 Identities=21% Similarity=0.482 Sum_probs=9.6
Q ss_pred CeecccCcCcCCCh
Q psy16685 13 PHVCSVCSKGFSTS 26 (99)
Q Consensus 13 ~~~C~~c~~~~~~~ 26 (99)
.+.|..||..|...
T Consensus 70 ~~~C~~CG~~~~~~ 83 (135)
T PRK03824 70 VLKCRNCGNEWSLK 83 (135)
T ss_pred EEECCCCCCEEecc
Confidence 46788888776553
No 100
>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=71.35 E-value=2.1 Score=16.62 Aligned_cols=10 Identities=40% Similarity=0.982 Sum_probs=6.7
Q ss_pred Cceecccccc
Q psy16685 40 KPHQCQVCGK 49 (99)
Q Consensus 40 ~~~~C~~C~~ 49 (99)
.+|.|+.||.
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4677777763
No 101
>KOG2482|consensus
Probab=71.05 E-value=3.4 Score=27.09 Aligned_cols=29 Identities=28% Similarity=0.493 Sum_probs=23.6
Q ss_pred eecccccccccCcchHHHHHHh--ccCCCcc
Q psy16685 42 HQCQVCGKRFTASSNLYYHRMT--HIKVNDD 70 (99)
Q Consensus 42 ~~C~~C~~~f~~~~~l~~H~~~--h~~~~~~ 70 (99)
++|..|.+.|..+..|+.||+. |....|.
T Consensus 196 ~~CLyCekifrdkntLkeHMrkK~HrrinPk 226 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRKKRHRRINPK 226 (423)
T ss_pred heeeeeccccCCcHHHHHHHHhccCcccCCC
Confidence 6899999999999999999994 5444443
No 102
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=70.22 E-value=3.3 Score=27.79 Aligned_cols=32 Identities=25% Similarity=0.648 Sum_probs=23.0
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcch
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSN 56 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~ 56 (99)
..|+.||....++ |..-|+|..|+..+.....
T Consensus 351 p~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 351 PVCPRCGGRMKSA-----------GRNGFRCKKCGTRARETLI 382 (421)
T ss_pred CCCCccCCchhhc-----------CCCCcccccccccCCcccc
Confidence 3799999776543 2337999999988776543
No 103
>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=69.55 E-value=1.8 Score=18.49 Aligned_cols=9 Identities=22% Similarity=1.054 Sum_probs=5.5
Q ss_pred ecccCcCcC
Q psy16685 15 VCSVCSKGF 23 (99)
Q Consensus 15 ~C~~c~~~~ 23 (99)
.|+.||.+|
T Consensus 3 ~C~~Cg~~Y 11 (36)
T PF05191_consen 3 ICPKCGRIY 11 (36)
T ss_dssp EETTTTEEE
T ss_pred CcCCCCCcc
Confidence 466666655
No 104
>KOG4167|consensus
Probab=69.44 E-value=1 Score=32.17 Aligned_cols=25 Identities=32% Similarity=0.458 Sum_probs=22.8
Q ss_pred ceecccccccccCcchHHHHHHhcc
Q psy16685 41 PHQCQVCGKRFTASSNLYYHRMTHI 65 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~h~ 65 (99)
.|.|..|++.|..-..+..||++|-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4899999999999999999999885
No 105
>PF15269 zf-C2H2_7: Zinc-finger
Probab=69.40 E-value=3.1 Score=18.75 Aligned_cols=22 Identities=23% Similarity=0.380 Sum_probs=18.0
Q ss_pred eecccccccccCcchHHHHHHh
Q psy16685 42 HQCQVCGKRFTASSNLYYHRMT 63 (99)
Q Consensus 42 ~~C~~C~~~f~~~~~l~~H~~~ 63 (99)
|+|-.|..+...++.|-.||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5788888888888888888874
No 106
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.85 E-value=2.1 Score=23.25 Aligned_cols=28 Identities=18% Similarity=0.253 Sum_probs=20.3
Q ss_pred ecccCcCcCCChHHHHHHhhhcCCCCceecccccccccC
Q psy16685 15 VCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTA 53 (99)
Q Consensus 15 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 53 (99)
.|+.||+.|.. ....|..|+.||++|..
T Consensus 11 idPetg~KFYD-----------LNrdPiVsPytG~s~P~ 38 (129)
T COG4530 11 IDPETGKKFYD-----------LNRDPIVSPYTGKSYPR 38 (129)
T ss_pred cCccccchhhc-----------cCCCccccCcccccchH
Confidence 47788877643 34578899999999843
No 107
>KOG2785|consensus
Probab=67.46 E-value=9.9 Score=25.27 Aligned_cols=53 Identities=19% Similarity=0.287 Sum_probs=42.1
Q ss_pred CCeecccCcCcCCChHHHHHHhhhcCCC-----------------------Cceeccccc---ccccCcchHHHHHHhc
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRRIHSGE-----------------------KPHQCQVCG---KRFTASSNLYYHRMTH 64 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~h 64 (99)
-|-.|-.|++.+.+-..-..|+..++|- .-+.|..|. +.|.+-.+.+.||...
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K 243 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDK 243 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhc
Confidence 3556899999998887778898887763 126788888 8899999999999853
No 108
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=67.30 E-value=4.1 Score=23.49 Aligned_cols=34 Identities=15% Similarity=0.114 Sum_probs=16.0
Q ss_pred CceecccccccccCcchHHHHHHhccCCCcchhhhcccc
Q psy16685 40 KPHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNLE 78 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~ 78 (99)
-+|.|. |+..|.+. .+|=..--|+ .|.|..|+..
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 356666 66554433 2222222344 5666666543
No 109
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=67.23 E-value=5.8 Score=17.90 Aligned_cols=32 Identities=16% Similarity=0.446 Sum_probs=18.1
Q ss_pred ecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCc
Q psy16685 15 VCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTAS 54 (99)
Q Consensus 15 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 54 (99)
-|+.||....... ..+...+.|+.||..+.-.
T Consensus 2 FCp~Cg~~l~~~~--------~~~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPKE--------GKEKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCcccccc--------CCCCCEEECCcCCCeEECC
Confidence 3778876443221 0112368899998765543
No 110
>KOG3507|consensus
Probab=66.89 E-value=4.3 Score=19.42 Aligned_cols=29 Identities=21% Similarity=0.516 Sum_probs=19.0
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
.|.|..|+..-.. ....++.|..||....
T Consensus 20 iYiCgdC~~en~l-----------k~~D~irCReCG~RIl 48 (62)
T KOG3507|consen 20 IYICGDCGQENTL-----------KRGDVIRCRECGYRIL 48 (62)
T ss_pred EEEeccccccccc-----------cCCCcEehhhcchHHH
Confidence 4889999854321 1235789999997644
No 111
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=66.57 E-value=0.89 Score=19.87 Aligned_cols=11 Identities=36% Similarity=0.887 Sum_probs=8.0
Q ss_pred ceecccccccc
Q psy16685 41 PHQCQVCGKRF 51 (99)
Q Consensus 41 ~~~C~~C~~~f 51 (99)
-|.|..|+..+
T Consensus 28 fy~C~~C~~~w 38 (40)
T smart00440 28 FYVCTKCGHRW 38 (40)
T ss_pred EEEeCCCCCEe
Confidence 37888888665
No 112
>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=66.25 E-value=5.4 Score=19.29 Aligned_cols=14 Identities=21% Similarity=0.617 Sum_probs=9.0
Q ss_pred CCceeccccccccc
Q psy16685 39 EKPHQCQVCGKRFT 52 (99)
Q Consensus 39 ~~~~~C~~C~~~f~ 52 (99)
.+.|.|+.||..+.
T Consensus 44 ~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 44 GRVFTCPNCGFEMD 57 (69)
T ss_pred cceEEcCCCCCEEC
Confidence 45677777776543
No 113
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=66.03 E-value=3.8 Score=18.88 Aligned_cols=12 Identities=25% Similarity=0.576 Sum_probs=8.5
Q ss_pred Cceecccccccc
Q psy16685 40 KPHQCQVCGKRF 51 (99)
Q Consensus 40 ~~~~C~~C~~~f 51 (99)
..+.|..|+..+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 467888888654
No 114
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=65.86 E-value=3.7 Score=17.85 Aligned_cols=21 Identities=19% Similarity=0.370 Sum_probs=14.5
Q ss_pred CCceecccccccccCcchHHH
Q psy16685 39 EKPHQCQVCGKRFTASSNLYY 59 (99)
Q Consensus 39 ~~~~~C~~C~~~f~~~~~l~~ 59 (99)
.....|+.|+..+.....|..
T Consensus 17 ~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 17 VEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEEEECCCCCeEEccHHHHHH
Confidence 345678888888777666644
No 115
>KOG2593|consensus
Probab=65.84 E-value=7 Score=26.38 Aligned_cols=42 Identities=19% Similarity=0.186 Sum_probs=24.1
Q ss_pred CCceecccccccccCcchHHHHHHhccCCCcchhhhccccccCCC
Q psy16685 39 EKPHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNLEPVSGS 83 (99)
Q Consensus 39 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~ 83 (99)
..-|.|+.|.+.|..-..++ -.-.....|.|..|+-.-....
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~gelveDe 167 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGGELVEDE 167 (436)
T ss_pred cccccCCccccchhhhHHHH---hhcccCceEEEecCCCchhccc
Confidence 45577777777766544432 2333445677777776544433
No 116
>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=65.49 E-value=2.9 Score=22.76 Aligned_cols=11 Identities=36% Similarity=0.667 Sum_probs=5.5
Q ss_pred eecccCcCcCC
Q psy16685 14 HVCSVCSKGFS 24 (99)
Q Consensus 14 ~~C~~c~~~~~ 24 (99)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 34555554443
No 117
>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=65.28 E-value=2.6 Score=19.81 Aligned_cols=31 Identities=19% Similarity=0.499 Sum_probs=19.9
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
+.|+.||..+...... .| ....|+.||..+-
T Consensus 3 ~~CP~CG~~iev~~~~-------~G-eiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENPE-------LG-ELVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCCc-------cC-CEEeCCCCCCEEE
Confidence 5799999876543321 12 3568999987653
No 118
>PLN02294 cytochrome c oxidase subunit Vb
Probab=65.25 E-value=3.6 Score=24.15 Aligned_cols=15 Identities=33% Similarity=0.722 Sum_probs=11.0
Q ss_pred CCCeecccCcCcCCC
Q psy16685 11 EKPHVCSVCSKGFST 25 (99)
Q Consensus 11 ~~~~~C~~c~~~~~~ 25 (99)
.+|+.|++||..|..
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 357788888887754
No 119
>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=64.42 E-value=3.2 Score=18.22 Aligned_cols=29 Identities=14% Similarity=0.193 Sum_probs=17.9
Q ss_pred eecccccccccCcchHHHHHHhccCCCcchhhhccc
Q psy16685 42 HQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNL 77 (99)
Q Consensus 42 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~ 77 (99)
|.|..||..|....... . ..+-.|-.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~------~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSIS------E-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcC------C-CCCCcCCCCCC
Confidence 78999998876554321 1 34555656654
No 120
>KOG3408|consensus
Probab=64.38 E-value=4.7 Score=22.29 Aligned_cols=23 Identities=26% Similarity=0.535 Sum_probs=12.2
Q ss_pred CCeecccCcCcCCChHHHHHHhh
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRR 34 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~ 34 (99)
..|.|-.|.+-|.+...++.|.+
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHh
Confidence 34555555555555555555544
No 121
>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=63.87 E-value=4.8 Score=17.88 Aligned_cols=12 Identities=33% Similarity=1.005 Sum_probs=7.2
Q ss_pred ecccCcCcCCCh
Q psy16685 15 VCSVCSKGFSTS 26 (99)
Q Consensus 15 ~C~~c~~~~~~~ 26 (99)
.|..|++.|.-.
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 366777666543
No 122
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=63.69 E-value=2.3 Score=22.69 Aligned_cols=40 Identities=20% Similarity=0.423 Sum_probs=24.1
Q ss_pred CCCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCc
Q psy16685 11 EKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTAS 54 (99)
Q Consensus 11 ~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 54 (99)
.+.|.|+.|+..-.+...++ .....-...|..||..|...
T Consensus 20 ~k~FtCp~Cghe~vs~ctvk----k~~~~g~~~Cg~CGls~e~e 59 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVK----KTVNIGTAVCGNCGLSFECE 59 (104)
T ss_pred CceEecCccCCeeeeEEEEE----ecCceeEEEcccCcceEEEe
Confidence 45688999987655433322 11222345789998877643
No 123
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=63.66 E-value=5.7 Score=17.41 Aligned_cols=23 Identities=22% Similarity=0.616 Sum_probs=13.6
Q ss_pred eeccccccccc--CcchHHHHHHhc
Q psy16685 42 HQCQVCGKRFT--ASSNLYYHRMTH 64 (99)
Q Consensus 42 ~~C~~C~~~f~--~~~~l~~H~~~h 64 (99)
..|+.||..|. ....-..|.+.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 47777776655 344455565554
No 124
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=63.56 E-value=4 Score=23.01 Aligned_cols=25 Identities=32% Similarity=0.527 Sum_probs=19.2
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKP 41 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~ 41 (99)
..|-++|+.|.+ |++|+.+|.+.-|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 358888988864 7889999888654
No 125
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=61.98 E-value=2.6 Score=23.51 Aligned_cols=35 Identities=26% Similarity=0.615 Sum_probs=21.5
Q ss_pred ecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCc
Q psy16685 15 VCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTAS 54 (99)
Q Consensus 15 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 54 (99)
.|+.|+........ ..-.+...|.|..|++.|...
T Consensus 32 ~cP~C~s~~~~k~g-----~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 32 NCPRCKSSNVVKIG-----GIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred cCCCCCccceeeEC-----CccccccccccCCcCcceeee
Confidence 58888765411111 112235679999999988754
No 126
>KOG2593|consensus
Probab=60.28 E-value=6.5 Score=26.53 Aligned_cols=40 Identities=20% Similarity=0.492 Sum_probs=27.7
Q ss_pred hcCCCCeecccCcCcCCChHHHHHHhhhcCCCCceeccccccc
Q psy16685 8 LISEKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKR 50 (99)
Q Consensus 8 h~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 50 (99)
-+...-|.|+.|.+.|.....++. .-...--|.|..|+..
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQL---LDNETGEFHCENCGGE 162 (436)
T ss_pred ccccccccCCccccchhhhHHHHh---hcccCceEEEecCCCc
Confidence 344567999999999988776542 1222346899988764
No 127
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=60.25 E-value=4.4 Score=15.37 Aligned_cols=6 Identities=50% Similarity=1.514 Sum_probs=2.8
Q ss_pred cccccc
Q psy16685 44 CQVCGK 49 (99)
Q Consensus 44 C~~C~~ 49 (99)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 444543
No 128
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=59.89 E-value=4.5 Score=21.96 Aligned_cols=10 Identities=30% Similarity=0.464 Sum_probs=4.8
Q ss_pred eecccCcCcC
Q psy16685 14 HVCSVCSKGF 23 (99)
Q Consensus 14 ~~C~~c~~~~ 23 (99)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 3455555443
No 129
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=59.83 E-value=5.3 Score=22.42 Aligned_cols=15 Identities=40% Similarity=0.988 Sum_probs=12.6
Q ss_pred CeecccCcCcCCChH
Q psy16685 13 PHVCSVCSKGFSTSS 27 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~ 27 (99)
|+.|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678999999998654
No 130
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=59.65 E-value=6.6 Score=18.26 Aligned_cols=39 Identities=23% Similarity=0.600 Sum_probs=19.4
Q ss_pred CCeeccc--CcCcCCChHHHHHHhhhcCCCCceeccc----ccccc
Q psy16685 12 KPHVCSV--CSKGFSTSSSLNTHRRIHSGEKPHQCQV----CGKRF 51 (99)
Q Consensus 12 ~~~~C~~--c~~~~~~~~~l~~h~~~~~~~~~~~C~~----C~~~f 51 (99)
.+..|+. |...+. ...|..|....=...+..|+. |...+
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~ 52 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERV 52 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EE
T ss_pred CEeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCcc
Confidence 4556766 333333 445677777544456677776 66554
No 131
>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=59.43 E-value=7.3 Score=16.88 Aligned_cols=32 Identities=25% Similarity=0.662 Sum_probs=14.7
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceeccccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKR 50 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 50 (99)
|..|..|+..+.. ......+.+.|.|..|+..
T Consensus 2 p~rC~~C~aylNp------~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 2 PVRCRRCRAYLNP------FCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp S-B-TTT--BS-T------TSEEETTTTEEEETTT--E
T ss_pred ccccCCCCCEECC------cceEcCCCCEEECcCCCCc
Confidence 4567777543322 2233445577888888764
No 132
>KOG1146|consensus
Probab=58.97 E-value=3.8 Score=31.45 Aligned_cols=52 Identities=21% Similarity=0.445 Sum_probs=40.6
Q ss_pred CCCeecccCcCcCCChHHHHHHhhhcC-----------------CCCceecccccccccCcchHHHHHHh
Q psy16685 11 EKPHVCSVCSKGFSTSSSLNTHRRIHS-----------------GEKPHQCQVCGKRFTASSNLYYHRMT 63 (99)
Q Consensus 11 ~~~~~C~~c~~~~~~~~~l~~h~~~~~-----------------~~~~~~C~~C~~~f~~~~~l~~H~~~ 63 (99)
..+|.|..|...|.....+..|.+... ...+| |..|...|.....|..|++.
T Consensus 1282 ~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~ 1350 (1406)
T KOG1146|consen 1282 THRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRS 1350 (1406)
T ss_pred chhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHH
Confidence 457889999888888887777765321 12346 99999999999999999996
No 133
>KOG2907|consensus
Probab=58.06 E-value=8.6 Score=21.00 Aligned_cols=12 Identities=33% Similarity=0.775 Sum_probs=8.1
Q ss_pred eecccccccccC
Q psy16685 42 HQCQVCGKRFTA 53 (99)
Q Consensus 42 ~~C~~C~~~f~~ 53 (99)
|.|+.|++.|..
T Consensus 103 YTC~kC~~k~~e 114 (116)
T KOG2907|consen 103 YTCPKCKYKFTE 114 (116)
T ss_pred EEcCccceeeec
Confidence 677777766643
No 134
>KOG0978|consensus
Probab=57.24 E-value=4.5 Score=29.01 Aligned_cols=22 Identities=23% Similarity=0.517 Sum_probs=15.3
Q ss_pred CCceecccccccccCcchHHHH
Q psy16685 39 EKPHQCQVCGKRFTASSNLYYH 60 (99)
Q Consensus 39 ~~~~~C~~C~~~f~~~~~l~~H 60 (99)
.+--+||.|+.+|+..+.+..|
T Consensus 676 tRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 676 TRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred HhcCCCCCCCCCCCcccccccC
Confidence 3445899999988877655443
No 135
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=57.10 E-value=11 Score=20.53 Aligned_cols=19 Identities=26% Similarity=0.585 Sum_probs=12.6
Q ss_pred CeecccCcCcCCChHHHHH
Q psy16685 13 PHVCSVCSKGFSTSSSLNT 31 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~ 31 (99)
|..|+.|+-...++..|.+
T Consensus 15 P~~CpiCgLtLVss~HLAR 33 (112)
T TIGR00622 15 PVECPICGLTLILSTHLAR 33 (112)
T ss_pred CCcCCcCCCEEeccchHHH
Confidence 5667777777666666654
No 136
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=56.97 E-value=2.8 Score=30.03 Aligned_cols=57 Identities=18% Similarity=0.322 Sum_probs=39.9
Q ss_pred cccCcCcCCChHHHHHHhhhcCCCCcee-cccccccccCcchHHHHHHhccCCCcchhhhccccc
Q psy16685 16 CSVCSKGFSTSSSLNTHRRIHSGEKPHQ-CQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNLEP 79 (99)
Q Consensus 16 C~~c~~~~~~~~~l~~h~~~~~~~~~~~-C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~ 79 (99)
|.-||-.|+.-..+- .-+.++....|. |+.|.+-|..+.+.+-| ..|.-|..|++..
T Consensus 126 CT~CGPRfTIi~alP-YDR~nTsM~~F~lC~~C~~EY~dP~nRRfH------AQp~aCp~CGP~~ 183 (750)
T COG0068 126 CTNCGPRFTIIEALP-YDRENTSMADFPLCPFCDKEYKDPLNRRFH------AQPIACPKCGPHL 183 (750)
T ss_pred cCCCCcceeeeccCC-CCcccCccccCcCCHHHHHHhcCccccccc------cccccCcccCCCe
Confidence 888998888666553 234456666664 89998888777665444 4678888888743
No 137
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=56.65 E-value=3.1 Score=23.91 Aligned_cols=15 Identities=40% Similarity=0.908 Sum_probs=10.3
Q ss_pred ceecccccccccCcc
Q psy16685 41 PHQCQVCGKRFTASS 55 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~ 55 (99)
.-.|+.|+..|.+..
T Consensus 28 RReC~~C~~RFTTfE 42 (156)
T COG1327 28 RRECLECGERFTTFE 42 (156)
T ss_pred hhcccccccccchhh
Confidence 356888888777653
No 138
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.47 E-value=5.6 Score=21.74 Aligned_cols=11 Identities=36% Similarity=0.697 Sum_probs=5.7
Q ss_pred eecccCcCcCC
Q psy16685 14 HVCSVCSKGFS 24 (99)
Q Consensus 14 ~~C~~c~~~~~ 24 (99)
..|..|+..|.
T Consensus 72 ~~C~~Cg~~~~ 82 (117)
T PRK00564 72 LECKDCSHVFK 82 (117)
T ss_pred EEhhhCCCccc
Confidence 44666664443
No 139
>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=55.90 E-value=3.6 Score=17.60 Aligned_cols=30 Identities=20% Similarity=0.517 Sum_probs=16.5
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVC 47 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C 47 (99)
..|+.|+..- .+..|-....|...|.|..|
T Consensus 6 v~CP~C~s~~----~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQSTE----GVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCCC----cceeCCCCCCCCEeEecCcC
Confidence 3577776432 13344444455566777766
No 140
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=55.28 E-value=7.3 Score=20.90 Aligned_cols=37 Identities=27% Similarity=0.516 Sum_probs=18.2
Q ss_pred CCeecccCcCcCC--ChHHHHHHhhhcCCCCceecccccc
Q psy16685 12 KPHVCSVCSKGFS--TSSSLNTHRRIHSGEKPHQCQVCGK 49 (99)
Q Consensus 12 ~~~~C~~c~~~~~--~~~~l~~h~~~~~~~~~~~C~~C~~ 49 (99)
+|-.|+.||..-. ....+..+... .+.-.|.|..|+-
T Consensus 1 ~p~~CpYCg~~~~l~~~~~iYg~~~~-~~~~~y~C~~C~A 39 (102)
T PF11672_consen 1 KPIICPYCGGPAELVDGSEIYGHRYD-DGPYLYVCTPCDA 39 (102)
T ss_pred CCcccCCCCCeeEEcccchhcCccCC-CCceeEECCCCCc
Confidence 4667999986433 22222221111 1112378888763
No 141
>KOG4167|consensus
Probab=54.55 E-value=2 Score=30.89 Aligned_cols=26 Identities=31% Similarity=0.447 Sum_probs=22.0
Q ss_pred CCeecccCcCcCCChHHHHHHhhhcC
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRRIHS 37 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~~~~ 37 (99)
.-|.|.+|+++|-.-..+..|+++|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 35889999999988888888988874
No 142
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=54.36 E-value=18 Score=21.79 Aligned_cols=35 Identities=20% Similarity=0.396 Sum_probs=20.0
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceecccccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRF 51 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 51 (99)
-+.|+.|+ .-.....+ ++.......+.|..||..+
T Consensus 6 y~~Cp~Cg-~eev~hEV---ik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 6 YIECPSCG-SEEVSHEV---IKERGREPLVRCEECGTVH 40 (201)
T ss_pred EEECCCCC-cchhhHHH---HHhcCCceEEEccCCCcEe
Confidence 35799998 22222222 2222333567999999876
No 143
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=53.63 E-value=6.5 Score=17.03 Aligned_cols=15 Identities=20% Similarity=0.450 Sum_probs=12.1
Q ss_pred CeecccCcCcCCChH
Q psy16685 13 PHVCSVCSKGFSTSS 27 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~ 27 (99)
|+.|..|+..|-...
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 788999998887654
No 144
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.51 E-value=3.5 Score=20.86 Aligned_cols=31 Identities=23% Similarity=0.611 Sum_probs=18.7
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceeccccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKR 50 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 50 (99)
.|.|..|+..|. +.+++. ....-.|+.|+..
T Consensus 12 ~Y~c~~cg~~~d----vvq~~~---ddplt~ce~c~a~ 42 (82)
T COG2331 12 SYECTECGNRFD----VVQAMT---DDPLTTCEECGAR 42 (82)
T ss_pred EEeecccchHHH----HHHhcc---cCccccChhhChH
Confidence 478999987664 233322 2333468888754
No 145
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=53.18 E-value=5.5 Score=17.53 Aligned_cols=15 Identities=40% Similarity=0.986 Sum_probs=9.7
Q ss_pred CceecccccccccCc
Q psy16685 40 KPHQCQVCGKRFTAS 54 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~ 54 (99)
.|+.|..|+..|-..
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 588999999888754
No 146
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=51.28 E-value=10 Score=20.57 Aligned_cols=29 Identities=14% Similarity=0.469 Sum_probs=19.7
Q ss_pred ecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCc
Q psy16685 15 VCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTAS 54 (99)
Q Consensus 15 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 54 (99)
.|+.|+..|... ....|.|+.|+......
T Consensus 4 ~CP~C~seytY~-----------dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYH-----------DGTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEe-----------cCCeeECcccccccccc
Confidence 588888766432 23468999998776544
No 147
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=51.21 E-value=8.5 Score=20.94 Aligned_cols=10 Identities=20% Similarity=0.571 Sum_probs=5.5
Q ss_pred eecccCcCcC
Q psy16685 14 HVCSVCSKGF 23 (99)
Q Consensus 14 ~~C~~c~~~~ 23 (99)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 4466666544
No 148
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.37 E-value=4.5 Score=25.02 Aligned_cols=40 Identities=25% Similarity=0.501 Sum_probs=25.1
Q ss_pred CCCeecccCcCcCCChHHHHHHhhhcCCC----------C-----ceeccccccc
Q psy16685 11 EKPHVCSVCSKGFSTSSSLNTHRRIHSGE----------K-----PHQCQVCGKR 50 (99)
Q Consensus 11 ~~~~~C~~c~~~~~~~~~l~~h~~~~~~~----------~-----~~~C~~C~~~ 50 (99)
++...|+.|+-.|.....+....++-.+. . .+.|+.|+.+
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~yA 71 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYYA 71 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhHH
Confidence 45688999998887665444444433322 1 2579999853
No 149
>KOG2807|consensus
Probab=50.36 E-value=26 Score=23.03 Aligned_cols=18 Identities=33% Similarity=0.696 Sum_probs=8.8
Q ss_pred CeecccCcCcCCChHHHH
Q psy16685 13 PHVCSVCSKGFSTSSSLN 30 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~ 30 (99)
|..|+.|+-.......|.
T Consensus 290 P~eCpiC~ltLVss~hLA 307 (378)
T KOG2807|consen 290 PIECPICSLTLVSSPHLA 307 (378)
T ss_pred CccCCccceeEecchHHH
Confidence 444555555544444443
No 150
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=50.26 E-value=13 Score=21.02 Aligned_cols=11 Identities=45% Similarity=1.346 Sum_probs=6.0
Q ss_pred ceecccccccc
Q psy16685 41 PHQCQVCGKRF 51 (99)
Q Consensus 41 ~~~C~~C~~~f 51 (99)
.|.|..|+..+
T Consensus 112 ~y~C~~C~~~~ 122 (146)
T smart00731 112 PYRCTGCGQRY 122 (146)
T ss_pred EEECCCCCCCC
Confidence 45566565443
No 151
>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=50.09 E-value=6.8 Score=22.15 Aligned_cols=10 Identities=30% Similarity=1.195 Sum_probs=4.7
Q ss_pred eecccccccc
Q psy16685 42 HQCQVCGKRF 51 (99)
Q Consensus 42 ~~C~~C~~~f 51 (99)
|.|..|+..+
T Consensus 124 ~~C~~C~~~~ 133 (157)
T PF10263_consen 124 YRCPSCGREY 133 (157)
T ss_pred EEcCCCCCEe
Confidence 4455555443
No 152
>KOG2071|consensus
Probab=49.75 E-value=9.7 Score=26.76 Aligned_cols=28 Identities=36% Similarity=0.646 Sum_probs=23.7
Q ss_pred CCceecccccccccCcchHHHHHHhccC
Q psy16685 39 EKPHQCQVCGKRFTASSNLYYHRMTHIK 66 (99)
Q Consensus 39 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 66 (99)
..|-.|..||..|........||..|..
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhhh
Confidence 4567899999999999988888888764
No 153
>PRK10220 hypothetical protein; Provisional
Probab=49.44 E-value=14 Score=20.11 Aligned_cols=29 Identities=14% Similarity=0.524 Sum_probs=19.8
Q ss_pred ecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCc
Q psy16685 15 VCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTAS 54 (99)
Q Consensus 15 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 54 (99)
.|+.|+..|... ....|.|+.|+.-+...
T Consensus 5 ~CP~C~seytY~-----------d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYE-----------DNGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEc-----------CCCeEECCcccCcCCcc
Confidence 588888766432 23468999998776544
No 154
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=49.25 E-value=17 Score=17.12 Aligned_cols=26 Identities=35% Similarity=0.877 Sum_probs=17.1
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccccccc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRF 51 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 51 (99)
..|..|+..|.. +.....|+.|+..+
T Consensus 6 ~~C~~Cg~~~~~------------~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 6 CKCPVCGKKFKD------------GDDIVVCPECGAPY 31 (54)
T ss_pred ccChhhCCcccC------------CCCEEECCCCCCcc
Confidence 358888877743 33456788887654
No 155
>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=48.21 E-value=9 Score=16.80 Aligned_cols=12 Identities=42% Similarity=1.143 Sum_probs=9.3
Q ss_pred Cceecccccccc
Q psy16685 40 KPHQCQVCGKRF 51 (99)
Q Consensus 40 ~~~~C~~C~~~f 51 (99)
.+..|+.|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 467899998776
No 156
>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=48.13 E-value=6.1 Score=21.43 Aligned_cols=11 Identities=27% Similarity=0.742 Sum_probs=5.1
Q ss_pred eecccCcCcCC
Q psy16685 14 HVCSVCSKGFS 24 (99)
Q Consensus 14 ~~C~~c~~~~~ 24 (99)
..|..||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PF01155_consen 71 ARCRDCGHEFE 81 (113)
T ss_dssp EEETTTS-EEE
T ss_pred EECCCCCCEEe
Confidence 34555555544
No 157
>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=46.55 E-value=6.9 Score=18.07 Aligned_cols=13 Identities=15% Similarity=0.746 Sum_probs=6.6
Q ss_pred ecccCcCcCCChH
Q psy16685 15 VCSVCSKGFSTSS 27 (99)
Q Consensus 15 ~C~~c~~~~~~~~ 27 (99)
.|+.|++.|....
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 7999998887543
No 158
>PHA02998 RNA polymerase subunit; Provisional
Probab=46.35 E-value=4.8 Score=23.86 Aligned_cols=38 Identities=24% Similarity=0.624 Sum_probs=21.5
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCc----eecccccccccCc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKP----HQCQVCGKRFTAS 54 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~----~~C~~C~~~f~~~ 54 (99)
...|+.|+..-.....+ .+..+..| |.|..||..|..+
T Consensus 143 ~v~CPkCg~~~A~f~ql----QTRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMI----QTRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCCceEEEEE----eeccCCCCceEEEEcCCCCCccCCc
Confidence 35688887543332222 22223333 7899999887654
No 159
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=46.26 E-value=3.5 Score=16.64 Aligned_cols=8 Identities=63% Similarity=1.281 Sum_probs=3.9
Q ss_pred cccCcCcC
Q psy16685 16 CSVCSKGF 23 (99)
Q Consensus 16 C~~c~~~~ 23 (99)
|-.|++.|
T Consensus 3 CiDC~~~F 10 (28)
T PF08790_consen 3 CIDCSKDF 10 (28)
T ss_dssp ETTTTEEE
T ss_pred eecCCCCc
Confidence 44455444
No 160
>KOG1842|consensus
Probab=46.18 E-value=8.4 Score=26.22 Aligned_cols=26 Identities=19% Similarity=0.225 Sum_probs=19.0
Q ss_pred CceecccccccccCcchHHHHHHhcc
Q psy16685 40 KPHQCQVCGKRFTASSNLYYHRMTHI 65 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~~~l~~H~~~h~ 65 (99)
..|.|+.|...|...+.|..|....+
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH 39 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEH 39 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhc
Confidence 45778888888888788888877543
No 161
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=45.56 E-value=6.2 Score=17.59 Aligned_cols=9 Identities=22% Similarity=0.774 Sum_probs=5.0
Q ss_pred Cceeccccc
Q psy16685 40 KPHQCQVCG 48 (99)
Q Consensus 40 ~~~~C~~C~ 48 (99)
..|.|..|.
T Consensus 36 ~~~~C~~C~ 44 (46)
T PF12760_consen 36 GRYRCKACR 44 (46)
T ss_pred CeEECCCCC
Confidence 455665554
No 162
>KOG2636|consensus
Probab=45.24 E-value=18 Score=24.75 Aligned_cols=26 Identities=12% Similarity=0.263 Sum_probs=16.6
Q ss_pred hcCCCCeecccCc-CcCCChHHHHHHh
Q psy16685 8 LISEKPHVCSVCS-KGFSTSSSLNTHR 33 (99)
Q Consensus 8 h~~~~~~~C~~c~-~~~~~~~~l~~h~ 33 (99)
|--...|.|.+|| .++..+..+.+|-
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHh
Confidence 3444567777777 6666666676663
No 163
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=45.04 E-value=19 Score=16.61 Aligned_cols=13 Identities=38% Similarity=0.966 Sum_probs=8.3
Q ss_pred eecccccccccCc
Q psy16685 42 HQCQVCGKRFTAS 54 (99)
Q Consensus 42 ~~C~~C~~~f~~~ 54 (99)
|+|+.|+..|...
T Consensus 29 W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKCPKCGHEWKAS 41 (55)
T ss_pred EECCCCCCeeEcc
Confidence 6777777665544
No 164
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=44.92 E-value=11 Score=23.37 Aligned_cols=16 Identities=19% Similarity=0.270 Sum_probs=12.8
Q ss_pred CCCCeecccCcCcCCC
Q psy16685 10 SEKPHVCSVCSKGFST 25 (99)
Q Consensus 10 ~~~~~~C~~c~~~~~~ 25 (99)
..++..|++||..|..
T Consensus 178 EGkpqRCpECGqVFKL 193 (268)
T PTZ00043 178 EGFLYRCGECDQIFML 193 (268)
T ss_pred CCCCccCCCCCcEEEE
Confidence 3457899999999875
No 165
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=44.62 E-value=15 Score=26.79 Aligned_cols=11 Identities=36% Similarity=1.056 Sum_probs=5.9
Q ss_pred Cceeccccccc
Q psy16685 40 KPHQCQVCGKR 50 (99)
Q Consensus 40 ~~~~C~~C~~~ 50 (99)
.|..|+.||..
T Consensus 474 ~p~~Cp~Cgs~ 484 (730)
T COG1198 474 IPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCC
Confidence 45556666543
No 166
>COG1773 Rubredoxin [Energy production and conversion]
Probab=44.39 E-value=10 Score=17.91 Aligned_cols=15 Identities=27% Similarity=0.576 Sum_probs=11.7
Q ss_pred CeecccCcCcCCChH
Q psy16685 13 PHVCSVCSKGFSTSS 27 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~ 27 (99)
.|.|..||..|.-..
T Consensus 3 ~~~C~~CG~vYd~e~ 17 (55)
T COG1773 3 RWRCSVCGYVYDPEK 17 (55)
T ss_pred ceEecCCceEecccc
Confidence 588999998886554
No 167
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=43.72 E-value=7.4 Score=26.61 Aligned_cols=16 Identities=25% Similarity=0.470 Sum_probs=10.7
Q ss_pred CCCeecccCcCcCCCh
Q psy16685 11 EKPHVCSVCSKGFSTS 26 (99)
Q Consensus 11 ~~~~~C~~c~~~~~~~ 26 (99)
...|.|..||..+...
T Consensus 423 ~~~~~c~~c~~~yd~~ 438 (479)
T PRK05452 423 GPRMQCSVCQWIYDPA 438 (479)
T ss_pred CCeEEECCCCeEECCC
Confidence 3467788887776644
No 168
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=43.60 E-value=17 Score=24.97 Aligned_cols=27 Identities=22% Similarity=0.441 Sum_probs=22.8
Q ss_pred CceecccccccccCcchHHHHHHh-ccC
Q psy16685 40 KPHQCQVCGKRFTASSNLYYHRMT-HIK 66 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~~~l~~H~~~-h~~ 66 (99)
+=|.|+.|.+.|.....+..|+.. |.+
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 457899999999999999999985 544
No 169
>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=43.59 E-value=10 Score=21.70 Aligned_cols=29 Identities=28% Similarity=0.659 Sum_probs=15.5
Q ss_pred CCeecccCcCcCCChHHHHHHhhhcCCCCceeccccccc
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKR 50 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 50 (99)
..|.|..||..... .+. ...-.|+.|+..
T Consensus 111 G~l~C~~Cg~~~~~---------~~~-~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 111 GTLVCENCGHEVEL---------THP-ERLPPCPKCGHT 139 (146)
T ss_pred ceEecccCCCEEEe---------cCC-CcCCCCCCCCCC
Confidence 35777777754321 112 234567777753
No 170
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=43.28 E-value=21 Score=22.78 Aligned_cols=11 Identities=27% Similarity=0.612 Sum_probs=6.2
Q ss_pred eeccccccccc
Q psy16685 42 HQCQVCGKRFT 52 (99)
Q Consensus 42 ~~C~~C~~~f~ 52 (99)
|.|+.|.-.|.
T Consensus 256 yvCs~Clsi~C 266 (279)
T TIGR00627 256 FVCSVCLSVLC 266 (279)
T ss_pred EECCCccCCcC
Confidence 66666655544
No 171
>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=43.12 E-value=19 Score=24.60 Aligned_cols=23 Identities=22% Similarity=0.585 Sum_probs=16.4
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceecccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGK 49 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 49 (99)
.|.|..||.... ...++|+.|+.
T Consensus 7 ~y~C~~Cg~~~~--------------~~~g~Cp~C~~ 29 (454)
T TIGR00416 7 KFVCQHCGADSP--------------KWQGKCPACHA 29 (454)
T ss_pred eEECCcCCCCCc--------------cccEECcCCCC
Confidence 599999986542 23578998863
No 172
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=42.52 E-value=0.76 Score=19.96 Aligned_cols=10 Identities=40% Similarity=1.006 Sum_probs=7.2
Q ss_pred eecccccccc
Q psy16685 42 HQCQVCGKRF 51 (99)
Q Consensus 42 ~~C~~C~~~f 51 (99)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 6788887654
No 173
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=42.02 E-value=6.1 Score=16.64 Aligned_cols=11 Identities=27% Similarity=0.628 Sum_probs=7.0
Q ss_pred Cceeccccccc
Q psy16685 40 KPHQCQVCGKR 50 (99)
Q Consensus 40 ~~~~C~~C~~~ 50 (99)
..+.|+.|+..
T Consensus 21 ~R~vC~~Cg~I 31 (34)
T PF14803_consen 21 ERLVCPACGFI 31 (34)
T ss_dssp -EEEETTTTEE
T ss_pred cceECCCCCCE
Confidence 45678888754
No 174
>PRK11823 DNA repair protein RadA; Provisional
Probab=41.72 E-value=19 Score=24.43 Aligned_cols=24 Identities=25% Similarity=0.588 Sum_probs=16.9
Q ss_pred CCeecccCcCcCCChHHHHHHhhhcCCCCceecccccc
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGK 49 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 49 (99)
..|.|..||.... ...++|+.|+.
T Consensus 6 ~~y~C~~Cg~~~~--------------~~~g~Cp~C~~ 29 (446)
T PRK11823 6 TAYVCQECGAESP--------------KWLGRCPECGA 29 (446)
T ss_pred CeEECCcCCCCCc--------------ccCeeCcCCCC
Confidence 4699999986542 23468998864
No 175
>PRK04351 hypothetical protein; Provisional
Probab=41.64 E-value=17 Score=20.83 Aligned_cols=31 Identities=16% Similarity=0.215 Sum_probs=18.0
Q ss_pred ceecccccccccCcchHHHHHHhccCCCcchhhhccccc
Q psy16685 41 PHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNLEP 79 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~ 79 (99)
.|.|..|+..+.+.. + .....+.|..|+...
T Consensus 112 ~Y~C~~Cg~~~~r~R------r--~n~~~yrCg~C~g~L 142 (149)
T PRK04351 112 LYECQSCGQQYLRKR------R--INTKRYRCGKCRGKL 142 (149)
T ss_pred EEECCCCCCEeeeee------e--cCCCcEEeCCCCcEe
Confidence 477877876554321 1 134667777777543
No 176
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=41.55 E-value=31 Score=14.39 Aligned_cols=22 Identities=23% Similarity=0.433 Sum_probs=10.9
Q ss_pred ceecccccccccCcchHHHHHHh
Q psy16685 41 PHQCQVCGKRFTASSNLYYHRMT 63 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~ 63 (99)
.+.|+.|++.+. .+-+..|...
T Consensus 4 ~~~C~nC~R~v~-a~RfA~HLek 25 (33)
T PF08209_consen 4 YVECPNCGRPVA-ASRFAPHLEK 25 (33)
T ss_dssp EEE-TTTSSEEE-GGGHHHHHHH
T ss_pred eEECCCCcCCcc-hhhhHHHHHH
Confidence 356666666543 2335555543
No 177
>PRK12496 hypothetical protein; Provisional
Probab=41.07 E-value=15 Score=21.34 Aligned_cols=11 Identities=27% Similarity=0.918 Sum_probs=6.2
Q ss_pred eeccccccccc
Q psy16685 42 HQCQVCGKRFT 52 (99)
Q Consensus 42 ~~C~~C~~~f~ 52 (99)
+.|..|++.|.
T Consensus 128 ~~C~gC~~~~~ 138 (164)
T PRK12496 128 KVCKGCKKKYP 138 (164)
T ss_pred EECCCCCcccc
Confidence 45666665553
No 178
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.80 E-value=18 Score=22.91 Aligned_cols=16 Identities=19% Similarity=0.478 Sum_probs=11.2
Q ss_pred CCceecccccccccCc
Q psy16685 39 EKPHQCQVCGKRFTAS 54 (99)
Q Consensus 39 ~~~~~C~~C~~~f~~~ 54 (99)
.+.|.|+.||..+...
T Consensus 320 ~r~~~C~~cg~~~~rD 335 (364)
T COG0675 320 GRLFKCPRCGFVHDRD 335 (364)
T ss_pred ceeEECCCCCCeehhh
Confidence 4568898888765543
No 179
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=40.70 E-value=13 Score=19.88 Aligned_cols=35 Identities=26% Similarity=0.387 Sum_probs=20.0
Q ss_pred CCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccC
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTA 53 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 53 (99)
.-+.|+.|+. ....-.+ ..+.....|+.||..+..
T Consensus 20 t~f~CP~Cge-~~v~v~~------~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGK-VSISVKI------KKNIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCC-eEeeeec------CCCcceEECCCCCCccCE
Confidence 3577999983 2221111 113345689999877654
No 180
>KOG0717|consensus
Probab=40.49 E-value=16 Score=25.07 Aligned_cols=22 Identities=32% Similarity=0.608 Sum_probs=19.3
Q ss_pred eecccccccccCcchHHHHHHh
Q psy16685 42 HQCQVCGKRFTASSNLYYHRMT 63 (99)
Q Consensus 42 ~~C~~C~~~f~~~~~l~~H~~~ 63 (99)
+-|..|.++|.+..++..|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7799999999999999888764
No 181
>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=40.27 E-value=9.1 Score=21.68 Aligned_cols=14 Identities=36% Similarity=0.854 Sum_probs=9.6
Q ss_pred CCeecccCcCcCCC
Q psy16685 12 KPHVCSVCSKGFST 25 (99)
Q Consensus 12 ~~~~C~~c~~~~~~ 25 (99)
+|..|+.||..|..
T Consensus 111 ~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 111 KPQRCPECGQVFKL 124 (136)
T ss_dssp SEEEETTTEEEEEE
T ss_pred CccCCCCCCeEEEE
Confidence 46778888777653
No 182
>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=40.22 E-value=10 Score=17.63 Aligned_cols=23 Identities=17% Similarity=0.408 Sum_probs=12.3
Q ss_pred CCeecccCcCcCCChHHHHHHhh
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRR 34 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~ 34 (99)
..|.|+.|.+.|-..-.+-.|..
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTT
T ss_pred CeEECCCCCCccccCcChhhhcc
Confidence 46899999999887666555533
No 183
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.87 E-value=10 Score=18.32 Aligned_cols=45 Identities=16% Similarity=0.292 Sum_probs=23.8
Q ss_pred hhhhhcCCCCeecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 4 ILRVLISEKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 4 h~~~h~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
|..++.+..++.|+.-+-.+..+.-+. .. ..+.-..|+.|+..|.
T Consensus 15 ~~~I~~~~~~l~C~g~~~p~~HPrV~L---~m-g~~gev~CPYC~t~y~ 59 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPPNDHPRVFL---DM-GDEGEVVCPYCSTRYR 59 (62)
T ss_pred ceEEEeCCeeEEcCCCCCCCCCCEEEE---Ec-CCCCcEecCccccEEE
Confidence 334566677788876655443322110 01 1123357888887764
No 184
>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=38.72 E-value=29 Score=19.69 Aligned_cols=46 Identities=17% Similarity=0.297 Sum_probs=25.8
Q ss_pred eecccCcCcCCChHHH--HHHhhh---cCCCCceecccccccccCcchHHH
Q psy16685 14 HVCSVCSKGFSTSSSL--NTHRRI---HSGEKPHQCQVCGKRFTASSNLYY 59 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l--~~h~~~---~~~~~~~~C~~C~~~f~~~~~l~~ 59 (99)
-.|..|+..+.....- ..-+.. .....-|.|+.|++.|..-+...+
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHH
Confidence 4699998765433211 111110 011234789999999987665544
No 185
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=38.60 E-value=15 Score=20.29 Aligned_cols=10 Identities=20% Similarity=0.278 Sum_probs=5.6
Q ss_pred eecccCcCcCC
Q psy16685 14 HVCSVCSKGFS 24 (99)
Q Consensus 14 ~~C~~c~~~~~ 24 (99)
..| .|+..|.
T Consensus 71 ~~C-~Cg~~~~ 80 (124)
T PRK00762 71 IEC-ECGYEGV 80 (124)
T ss_pred EEe-eCcCccc
Confidence 456 6665554
No 186
>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=38.41 E-value=21 Score=24.68 Aligned_cols=10 Identities=40% Similarity=1.135 Sum_probs=5.8
Q ss_pred Cceecccccc
Q psy16685 40 KPHQCQVCGK 49 (99)
Q Consensus 40 ~~~~C~~C~~ 49 (99)
.|..|+.|+.
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 3556666654
No 187
>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=38.18 E-value=22 Score=17.03 Aligned_cols=28 Identities=32% Similarity=0.800 Sum_probs=10.8
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccccccccC
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTA 53 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 53 (99)
-.|..|++.|.. -.+..-|..||..|-.
T Consensus 10 ~~C~~C~~~F~~------------~~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 10 SNCMICGKKFSL------------FRRRHHCRNCGRVVCS 37 (69)
T ss_dssp SB-TTT--B-BS------------SS-EEE-TTT--EEEC
T ss_pred CcCcCcCCcCCC------------ceeeEccCCCCCEECC
Confidence 357778777742 1244566666665543
No 188
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=37.01 E-value=24 Score=16.31 Aligned_cols=10 Identities=30% Similarity=0.757 Sum_probs=7.0
Q ss_pred ceeccccccc
Q psy16685 41 PHQCQVCGKR 50 (99)
Q Consensus 41 ~~~C~~C~~~ 50 (99)
.|.|..||.+
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 5777777754
No 189
>PRK06260 threonine synthase; Validated
Probab=36.45 E-value=24 Score=23.45 Aligned_cols=27 Identities=26% Similarity=0.587 Sum_probs=15.9
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
+.|..||..|... ...+.|+.|+..+.
T Consensus 4 ~~C~~cg~~~~~~------------~~~~~Cp~cg~~l~ 30 (397)
T PRK06260 4 LKCIECGKEYDPD------------EIIYTCPECGGLLE 30 (397)
T ss_pred EEECCCCCCCCCC------------CccccCCCCCCeEE
Confidence 5677887766421 23466777765443
No 190
>PRK14873 primosome assembly protein PriA; Provisional
Probab=36.09 E-value=24 Score=25.48 Aligned_cols=10 Identities=30% Similarity=0.896 Sum_probs=5.6
Q ss_pred Cceecccccc
Q psy16685 40 KPHQCQVCGK 49 (99)
Q Consensus 40 ~~~~C~~C~~ 49 (99)
.|+.|+.|+.
T Consensus 421 ~p~~Cp~Cgs 430 (665)
T PRK14873 421 PDWRCPRCGS 430 (665)
T ss_pred cCccCCCCcC
Confidence 3556666654
No 191
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=35.43 E-value=18 Score=15.46 Aligned_cols=12 Identities=17% Similarity=0.321 Sum_probs=6.3
Q ss_pred CCeecccCcCcC
Q psy16685 12 KPHVCSVCSKGF 23 (99)
Q Consensus 12 ~~~~C~~c~~~~ 23 (99)
+-|.|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 358899998764
No 192
>PRK05978 hypothetical protein; Provisional
Probab=34.74 E-value=23 Score=20.42 Aligned_cols=10 Identities=50% Similarity=1.368 Sum_probs=4.7
Q ss_pred eccccccccc
Q psy16685 43 QCQVCGKRFT 52 (99)
Q Consensus 43 ~C~~C~~~f~ 52 (99)
.|+.||..|.
T Consensus 54 ~C~~CG~~~~ 63 (148)
T PRK05978 54 HCAACGEDFT 63 (148)
T ss_pred CccccCCccc
Confidence 4555554443
No 193
>KOG1280|consensus
Probab=34.65 E-value=44 Score=22.20 Aligned_cols=37 Identities=22% Similarity=0.386 Sum_probs=20.8
Q ss_pred CCeecccCcCcCCChHHHHHHhhhcCCCCc--eeccccc
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRRIHSGEKP--HQCQVCG 48 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~--~~C~~C~ 48 (99)
.-|.|+.|+..-.+...+..|+...+.+-+ ..|+.|+
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 357777777766666666666554322222 3455554
No 194
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG1088|consensus
Probab=33.66 E-value=22 Score=19.61 Aligned_cols=20 Identities=25% Similarity=0.328 Sum_probs=12.1
Q ss_pred hcCCCCeecccCcCcCCChH
Q psy16685 8 LISEKPHVCSVCSKGFSTSS 27 (99)
Q Consensus 8 h~~~~~~~C~~c~~~~~~~~ 27 (99)
+..+....|+.||..|+-+.
T Consensus 93 ~v~EG~l~CpetG~vfpI~~ 112 (124)
T KOG1088|consen 93 DVIEGELVCPETGRVFPISD 112 (124)
T ss_pred hhccceEecCCCCcEeeccc
Confidence 33445566777777776543
No 196
>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=33.26 E-value=17 Score=16.72 Aligned_cols=13 Identities=23% Similarity=0.915 Sum_probs=10.0
Q ss_pred eecccccccccCc
Q psy16685 42 HQCQVCGKRFTAS 54 (99)
Q Consensus 42 ~~C~~C~~~f~~~ 54 (99)
|+|..||..+...
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 6888998877644
No 197
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=32.98 E-value=8.9 Score=17.23 Aligned_cols=38 Identities=26% Similarity=0.443 Sum_probs=20.1
Q ss_pred ecccCcCcCCChHHHHHHhhhcCCCCceecc--cccccccCc
Q psy16685 15 VCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQ--VCGKRFTAS 54 (99)
Q Consensus 15 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~--~C~~~f~~~ 54 (99)
.|+.||........... .....+.-+.|. .||..|...
T Consensus 1 ~CP~Cg~~a~ir~S~~~--s~~~~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQL--SPLTRELYCQCTNPECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEEchhh--CcceEEEEEEECCCcCCCEEEEE
Confidence 37888866544432221 112223456775 488887643
No 198
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=32.93 E-value=2.9 Score=20.54 Aligned_cols=42 Identities=24% Similarity=0.487 Sum_probs=20.9
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchH
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNL 57 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l 57 (99)
.|.|..|+..-. ..+ .-...+.|....+|+.|.....-.++|
T Consensus 4 ~FTC~~C~~Rs~--~~~-sk~aY~~GvViv~C~gC~~~HlIaDnL 45 (66)
T PF05180_consen 4 TFTCNKCGTRSA--KMF-SKQAYHKGVVIVQCPGCKNRHLIADNL 45 (66)
T ss_dssp EEEETTTTEEEE--EEE-EHHHHHTSEEEEE-TTS--EEES--SS
T ss_pred EEEcCCCCCccc--eee-CHHHHhCCeEEEECCCCcceeeehhhh
Confidence 377888874322 111 123446677778999997654444433
No 199
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=32.46 E-value=33 Score=21.47 Aligned_cols=32 Identities=22% Similarity=0.496 Sum_probs=17.1
Q ss_pred ecccCcCcCCChHHHHHHhhhcCCCCceeccccccc
Q psy16685 15 VCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKR 50 (99)
Q Consensus 15 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 50 (99)
.|..|.-..+.. +..-++. +..+..|+.||+.
T Consensus 199 ~C~GC~m~l~~~--~~~~V~~--~d~iv~CP~CgRI 230 (239)
T COG1579 199 VCGGCHMKLPSQ--TLSKVRK--KDEIVFCPYCGRI 230 (239)
T ss_pred cccCCeeeecHH--HHHHHhc--CCCCccCCccchH
Confidence 466665444322 2222332 5566788888864
No 200
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=32.07 E-value=44 Score=14.96 Aligned_cols=30 Identities=33% Similarity=0.652 Sum_probs=18.0
Q ss_pred CCCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccc
Q psy16685 11 EKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRF 51 (99)
Q Consensus 11 ~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 51 (99)
..|-.|..|++.... .+...|.|..|+...
T Consensus 9 ~~~~~C~~C~~~i~g-----------~~~~g~~C~~C~~~~ 38 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWG-----------LGKQGYRCSWCGLVC 38 (53)
T ss_dssp SSTEB-TTSSSBECS-----------SSSCEEEETTTT-EE
T ss_pred CCCCCCcccCcccCC-----------CCCCeEEECCCCChH
Confidence 567788888876511 234567888877543
No 201
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=32.04 E-value=29 Score=20.59 Aligned_cols=8 Identities=38% Similarity=1.198 Sum_probs=4.6
Q ss_pred eecccccc
Q psy16685 42 HQCQVCGK 49 (99)
Q Consensus 42 ~~C~~C~~ 49 (99)
|.|+.||.
T Consensus 133 F~Cp~Cg~ 140 (176)
T COG1675 133 FTCPKCGE 140 (176)
T ss_pred CCCCCCCc
Confidence 56666654
No 202
>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=31.95 E-value=19 Score=16.37 Aligned_cols=36 Identities=25% Similarity=0.530 Sum_probs=17.5
Q ss_pred eecccCcCcCCChHHHHHHhhhcCC------CCceeccccccc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSG------EKPHQCQVCGKR 50 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~------~~~~~C~~C~~~ 50 (99)
|.|..|+.++.....-.. ..+..| ..-|.|+.|+..
T Consensus 2 y~C~~CgyvYd~~~Gd~~-~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPE-NGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETTTBBGG-GTB-TT--GGGS-TT-B-TTTSSB
T ss_pred cCCCCCCEEEcCCcCCcc-cCcCCCCCHHHCCCCCcCcCCCCc
Confidence 789999887765432111 011111 234788888743
No 203
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=31.92 E-value=55 Score=19.17 Aligned_cols=56 Identities=18% Similarity=0.311 Sum_probs=33.7
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceecc--cccccccCcchHHHHHHh-ccCCCcc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQ--VCGKRFTASSNLYYHRMT-HIKVNDD 70 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~--~C~~~f~~~~~l~~H~~~-h~~~~~~ 70 (99)
...|+.|-........+.. -+.+...|+..|. .|.+. .+...|..|.+. |...+|-
T Consensus 80 ~L~CPLCRG~V~GWtvve~-AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~~HP~~rP~ 138 (162)
T PF07800_consen 80 ELACPLCRGEVKGWTVVEP-ARRFLNAKKRSCSQESCSFS-GTYSELRKHARSEHPSARPS 138 (162)
T ss_pred cccCccccCceeceEEchH-HHHHhccCCccCcccccccc-cCHHHHHHHHHhhCCCCCCc
Confidence 4568888655444443322 4445566777775 35433 367789999885 5555554
No 204
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=31.80 E-value=49 Score=21.35 Aligned_cols=27 Identities=22% Similarity=0.245 Sum_probs=22.0
Q ss_pred CCceecccccccccCcchHHHHHHhcc
Q psy16685 39 EKPHQCQVCGKRFTASSNLYYHRMTHI 65 (99)
Q Consensus 39 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 65 (99)
...|.|..|-+-|.+...+.+|+....
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~C~ 72 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAKCD 72 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHhCC
Confidence 456899999999999999999987433
No 205
>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=31.70 E-value=24 Score=18.75 Aligned_cols=20 Identities=35% Similarity=0.858 Sum_probs=14.4
Q ss_pred hhhcCCCCceecccccccccC
Q psy16685 33 RRIHSGEKPHQCQVCGKRFTA 53 (99)
Q Consensus 33 ~~~~~~~~~~~C~~C~~~f~~ 53 (99)
+..+.+ +|.+|..||.-|.-
T Consensus 72 ~~l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 72 MWLEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EEEeCC-CceeCCCCCcEEEE
Confidence 334455 79999999987753
No 206
>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=31.48 E-value=90 Score=16.72 Aligned_cols=38 Identities=11% Similarity=0.191 Sum_probs=27.3
Q ss_pred CCeecccCcCcCCChHHHHHHhhhcCCCCceeccccccc
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKR 50 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 50 (99)
..|.|+.-+..|..-......+.. ...+.|.|...|+.
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~-y~~~vwtC~~TGk~ 39 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMIL-YNQRVWTCEITGKS 39 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHH-HhCCeeEEecCCCC
Confidence 457788888889887766655443 34578999887764
No 207
>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=30.93 E-value=32 Score=22.90 Aligned_cols=9 Identities=44% Similarity=0.722 Sum_probs=5.6
Q ss_pred eecccCcCc
Q psy16685 14 HVCSVCSKG 22 (99)
Q Consensus 14 ~~C~~c~~~ 22 (99)
|.|..||..
T Consensus 1 ~~c~~cg~~ 9 (372)
T cd01121 1 YVCSECGYV 9 (372)
T ss_pred CCCCCCCCC
Confidence 457777644
No 208
>PTZ00448 hypothetical protein; Provisional
Probab=30.72 E-value=31 Score=23.02 Aligned_cols=23 Identities=13% Similarity=0.297 Sum_probs=19.8
Q ss_pred ceecccccccccCcchHHHHHHh
Q psy16685 41 PHQCQVCGKRFTASSNLYYHRMT 63 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~ 63 (99)
.|.|..|+..|......+.|.+.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999888888888874
No 209
>KOG2857|consensus
Probab=30.23 E-value=24 Score=20.22 Aligned_cols=23 Identities=13% Similarity=0.352 Sum_probs=19.2
Q ss_pred CceecccccccccCcchHHHHHH
Q psy16685 40 KPHQCQVCGKRFTASSNLYYHRM 62 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~~~l~~H~~ 62 (99)
..|+|+.|...|.+-..++.|+.
T Consensus 16 ~KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 16 IKYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hhccCCCCCCccccchhhhhccC
Confidence 35899999988888888888876
No 210
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=30.11 E-value=27 Score=14.53 Aligned_cols=12 Identities=33% Similarity=0.841 Sum_probs=7.8
Q ss_pred CeecccCcCcCC
Q psy16685 13 PHVCSVCSKGFS 24 (99)
Q Consensus 13 ~~~C~~c~~~~~ 24 (99)
-+.|..|+.+|.
T Consensus 21 ~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 21 YEVCIFCGSSFP 32 (33)
T ss_pred eEEcccCCcEee
Confidence 345888877653
No 211
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=30.06 E-value=37 Score=22.29 Aligned_cols=42 Identities=21% Similarity=0.344 Sum_probs=23.2
Q ss_pred cCCCCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccC
Q psy16685 9 ISEKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTA 53 (99)
Q Consensus 9 ~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 53 (99)
+.++|..--.||.+... .++. +-...|...|+|+.|+..-..
T Consensus 347 t~ENpP~ml~CgHVIsk-eal~--~LS~nG~~~FKCPYCP~~~~~ 388 (396)
T COG5109 347 TDENPPVMLECGHVISK-EALS--VLSQNGVLSFKCPYCPEMSKY 388 (396)
T ss_pred cccCCCeeeeccceeeH-HHHH--HHhhcCcEEeeCCCCCcchhh
Confidence 34555555567665443 3332 233456678888888755433
No 212
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=29.95 E-value=13 Score=22.41 Aligned_cols=40 Identities=28% Similarity=0.389 Sum_probs=21.0
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCC---ceecccccccccCc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEK---PHQCQVCGKRFTAS 54 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~---~~~C~~C~~~f~~~ 54 (99)
...|+.||..+.....+. ---+.|.. .+.|..||+.+..-
T Consensus 14 ~~~CPvCg~~l~~~~~~~--~IPyFG~V~i~t~~C~~CgYR~~DV 56 (201)
T COG1779 14 RIDCPVCGGTLKAHMYLY--DIPYFGEVLISTGVCERCGYRSTDV 56 (201)
T ss_pred eecCCcccceeeEEEeee--cCCccceEEEEEEEccccCCcccce
Confidence 346999988544322211 01122321 25788898776543
No 213
>PHA02942 putative transposase; Provisional
Probab=29.94 E-value=36 Score=22.72 Aligned_cols=14 Identities=21% Similarity=0.589 Sum_probs=9.0
Q ss_pred CCceeccccccccc
Q psy16685 39 EKPHQCQVCGKRFT 52 (99)
Q Consensus 39 ~~~~~C~~C~~~f~ 52 (99)
.+.|.|+.||....
T Consensus 340 ~r~f~C~~CG~~~d 353 (383)
T PHA02942 340 HRYFHCPSCGYEND 353 (383)
T ss_pred CCEEECCCCCCEeC
Confidence 34677877776543
No 214
>KOG0696|consensus
Probab=29.88 E-value=26 Score=24.25 Aligned_cols=58 Identities=19% Similarity=0.313 Sum_probs=33.3
Q ss_pred CCCeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCcchHHHHHH-hccCCCcchhhhccc
Q psy16685 11 EKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYHRM-THIKVNDDFKEILNL 77 (99)
Q Consensus 11 ~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~-~h~~~~~~~~~~~~~ 77 (99)
+.-++|.+|. +..|.+.|. -..|.|+.-++.+.+......|.- +|+=..|-+|.-|+.
T Consensus 71 KQGfQCqvC~--------fvvHkrChe-fVtF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCGs 129 (683)
T KOG0696|consen 71 KQGFQCQVCC--------FVVHKRCHE-FVTFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCGS 129 (683)
T ss_pred cCceeeeEEe--------ehhhhhhcc-eEEEECCCCCCCCCCCCcccccceeeeecCCCchhhhHHH
Confidence 3445555553 234555542 245777766666666666666633 455566777766664
No 215
>PF12773 DZR: Double zinc ribbon
Probab=29.66 E-value=39 Score=14.98 Aligned_cols=11 Identities=27% Similarity=0.770 Sum_probs=6.7
Q ss_pred Cceeccccccc
Q psy16685 40 KPHQCQVCGKR 50 (99)
Q Consensus 40 ~~~~C~~C~~~ 50 (99)
....|+.|+..
T Consensus 28 ~~~~C~~Cg~~ 38 (50)
T PF12773_consen 28 SKKICPNCGAE 38 (50)
T ss_pred CCCCCcCCcCC
Confidence 34567777654
No 216
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=29.63 E-value=30 Score=23.04 Aligned_cols=33 Identities=15% Similarity=0.219 Sum_probs=22.6
Q ss_pred ecccccccccCcchHHHHHHhccCCCcchhhhcc
Q psy16685 43 QCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILN 76 (99)
Q Consensus 43 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~ 76 (99)
.|..|...|-....|.+|++..+ |+-+-|...+
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H-E~ChICD~v~ 254 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH-EACHICDMVG 254 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh-hhhhhhhccC
Confidence 58888888888888888888654 3444444333
No 217
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=29.57 E-value=36 Score=16.04 Aligned_cols=16 Identities=25% Similarity=0.704 Sum_probs=8.3
Q ss_pred CceecccccccccCcc
Q psy16685 40 KPHQCQVCGKRFTASS 55 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~~ 55 (99)
.|+....|+..|...+
T Consensus 23 ~PV~s~~C~H~fek~a 38 (57)
T PF11789_consen 23 DPVKSKKCGHTFEKEA 38 (57)
T ss_dssp SEEEESSS--EEEHHH
T ss_pred CCcCcCCCCCeecHHH
Confidence 4566666777665554
No 218
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=29.51 E-value=22 Score=19.26 Aligned_cols=23 Identities=30% Similarity=0.651 Sum_probs=13.5
Q ss_pred CCeecccCcCcCCChHHHHHHhh
Q psy16685 12 KPHVCSVCSKGFSTSSSLNTHRR 34 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~~h~~ 34 (99)
..+.|-.|.+-|.+...|..|.+
T Consensus 54 GqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhc
Confidence 34556666666666666655544
No 219
>KOG3362|consensus
Probab=28.50 E-value=14 Score=21.14 Aligned_cols=22 Identities=23% Similarity=0.502 Sum_probs=14.2
Q ss_pred ceecccccccccCcchHHHHHH
Q psy16685 41 PHQCQVCGKRFTASSNLYYHRM 62 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~ 62 (99)
+|.|..||..+.+-..+..|..
T Consensus 129 ~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 129 KYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred hhHHHhcCCceeechhhhhccc
Confidence 4566677777766666666644
No 220
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=27.99 E-value=16 Score=19.90 Aligned_cols=11 Identities=36% Similarity=0.996 Sum_probs=7.7
Q ss_pred eeccccccccc
Q psy16685 42 HQCQVCGKRFT 52 (99)
Q Consensus 42 ~~C~~C~~~f~ 52 (99)
|.|..||..+.
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 67877876653
No 221
>KOG1813|consensus
Probab=27.96 E-value=40 Score=21.88 Aligned_cols=15 Identities=33% Similarity=0.793 Sum_probs=8.1
Q ss_pred CceecccccccccCc
Q psy16685 40 KPHQCQVCGKRFTAS 54 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~ 54 (99)
.||.|..|...|..+
T Consensus 240 ~Pf~c~icr~~f~~p 254 (313)
T KOG1813|consen 240 LPFKCFICRKYFYRP 254 (313)
T ss_pred CCccccccccccccc
Confidence 356666665555443
No 222
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=27.24 E-value=28 Score=16.28 Aligned_cols=31 Identities=29% Similarity=0.501 Sum_probs=17.0
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceecccccc
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGK 49 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 49 (99)
.|.| .||..|.....-. ..+.....|..|..
T Consensus 18 ~y~C-RCG~~f~i~e~~l-----~~~~~iv~C~sCSL 48 (55)
T PF05207_consen 18 SYPC-RCGGEFEISEEDL-----EEGEVIVQCDSCSL 48 (55)
T ss_dssp EEEE-TTSSEEEEEHHHH-----HCT--EEEETTTTE
T ss_pred EEcC-CCCCEEEEcchhc-----cCcCEEEECCCCcc
Confidence 4668 7887776543321 12245677877754
No 223
>KOG2231|consensus
Probab=26.88 E-value=73 Score=23.21 Aligned_cols=47 Identities=21% Similarity=0.470 Sum_probs=31.0
Q ss_pred ecccCcCcCCChHHHHHHhhhcCCCCceeccccc------ccccCcchHHHHHHhcc
Q psy16685 15 VCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCG------KRFTASSNLYYHRMTHI 65 (99)
Q Consensus 15 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~------~~f~~~~~l~~H~~~h~ 65 (99)
.|..|...|.....+..|++.+ .|.|..|. .-|.....|..|-+.++
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~----h~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFD----HEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cchhhhhhhccHHHHHHhhccc----eeheeecCcccccchhcccchHHHHHhhhcC
Confidence 5788888888888888877643 34454442 34566677777766544
No 224
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=26.52 E-value=32 Score=20.95 Aligned_cols=15 Identities=27% Similarity=0.826 Sum_probs=10.6
Q ss_pred CceecccccccccCc
Q psy16685 40 KPHQCQVCGKRFTAS 54 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~ 54 (99)
.||.|..|.+.|.++
T Consensus 195 IPF~C~iCKkdy~sp 209 (259)
T COG5152 195 IPFLCGICKKDYESP 209 (259)
T ss_pred Cceeehhchhhccch
Confidence 578888877666554
No 225
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=26.52 E-value=51 Score=22.07 Aligned_cols=26 Identities=12% Similarity=0.257 Sum_probs=16.5
Q ss_pred hcCCCCeecccCc-CcCCChHHHHHHh
Q psy16685 8 LISEKPHVCSVCS-KGFSTSSSLNTHR 33 (99)
Q Consensus 8 h~~~~~~~C~~c~-~~~~~~~~l~~h~ 33 (99)
|--.+.|.|.+|| .++-....+.+|-
T Consensus 369 hgLd~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 369 HGLDIEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred cCCCcceeeeecccccccchHHHHhhh
Confidence 4445667788887 5666666666653
No 226
>PF14369 zf-RING_3: zinc-finger
Probab=26.16 E-value=32 Score=14.43 Aligned_cols=10 Identities=40% Similarity=1.092 Sum_probs=8.1
Q ss_pred ecccCcCcCC
Q psy16685 15 VCSVCSKGFS 24 (99)
Q Consensus 15 ~C~~c~~~~~ 24 (99)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4999998875
No 227
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=26.03 E-value=44 Score=15.88 Aligned_cols=37 Identities=19% Similarity=0.338 Sum_probs=19.0
Q ss_pred eecccCcCcCCChHH-H-HHHhhhcCCCCceecccccccc
Q psy16685 14 HVCSVCSKGFSTSSS-L-NTHRRIHSGEKPHQCQVCGKRF 51 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~-l-~~h~~~~~~~~~~~C~~C~~~f 51 (99)
..|..|++.+..... + ...++. ..-..|.|..|....
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrn-rPi~tYmC~eC~~RI 41 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRN-RPIHTYMCDECKERI 41 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhc-CCCcceeChhHHHHH
Confidence 467888877553321 1 112221 223458888886543
No 228
>PRK04023 DNA polymerase II large subunit; Validated
Probab=25.92 E-value=74 Score=24.55 Aligned_cols=9 Identities=33% Similarity=0.892 Sum_probs=5.5
Q ss_pred eecccCcCc
Q psy16685 14 HVCSVCSKG 22 (99)
Q Consensus 14 ~~C~~c~~~ 22 (99)
..|+.||..
T Consensus 627 RfCpsCG~~ 635 (1121)
T PRK04023 627 RKCPSCGKE 635 (1121)
T ss_pred ccCCCCCCc
Confidence 357777654
No 229
>PF12907 zf-met2: Zinc-binding
Probab=25.90 E-value=25 Score=15.40 Aligned_cols=20 Identities=25% Similarity=0.600 Sum_probs=9.0
Q ss_pred eccccccccc---CcchHHHHHH
Q psy16685 43 QCQVCGKRFT---ASSNLYYHRM 62 (99)
Q Consensus 43 ~C~~C~~~f~---~~~~l~~H~~ 62 (99)
.|..|-.+|. ....|..|-.
T Consensus 3 ~C~iC~qtF~~t~~~~~L~eH~e 25 (40)
T PF12907_consen 3 ICKICRQTFMQTTNEPQLKEHAE 25 (40)
T ss_pred CcHHhhHHHHhcCCHHHHHHHHH
Confidence 4555553333 2234555544
No 230
>KOG3352|consensus
Probab=25.87 E-value=30 Score=19.99 Aligned_cols=13 Identities=23% Similarity=0.669 Sum_probs=7.3
Q ss_pred CCeecccCcCcCC
Q psy16685 12 KPHVCSVCSKGFS 24 (99)
Q Consensus 12 ~~~~C~~c~~~~~ 24 (99)
+...|.+||..|.
T Consensus 132 e~~rc~eCG~~fk 144 (153)
T KOG3352|consen 132 ETQRCPECGHYFK 144 (153)
T ss_pred CcccCCcccceEE
Confidence 3445666665554
No 231
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.62 E-value=62 Score=15.71 Aligned_cols=40 Identities=18% Similarity=0.370 Sum_probs=18.7
Q ss_pred eecccCcCcC-CChHHHHHHhhhcCCCCceecccccccccC
Q psy16685 14 HVCSVCSKGF-STSSSLNTHRRIHSGEKPHQCQVCGKRFTA 53 (99)
Q Consensus 14 ~~C~~c~~~~-~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 53 (99)
..|.+|.+.- .....+..-.-....-.-|.|+.|......
T Consensus 3 vkCiiCd~v~~iD~rt~~tKrLrN~PIrtymC~eC~~Rva~ 43 (68)
T COG4896 3 VKCIICDRVDEIDNRTFKTKRLRNKPIRTYMCPECEHRVAI 43 (68)
T ss_pred ceEEEecceeeecchhHHHHHhhCCCceeEechhhHhhhch
Confidence 3577776542 222222211111222244788888755443
No 232
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=25.58 E-value=45 Score=21.42 Aligned_cols=31 Identities=19% Similarity=0.506 Sum_probs=19.4
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccccccccC
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTA 53 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 53 (99)
..|+.|+.....+. |. ...+.|+.|+.-|.-
T Consensus 27 ~~c~~c~~~~~~~~-l~--------~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 27 TKCPKCGQVLYTKE-LE--------RNLEVCPKCDHHMRM 57 (285)
T ss_pred eECCCCcchhhHHH-HH--------hhCCCCCCCCCcCcC
Confidence 46888887654333 11 234689999887653
No 233
>PRK06450 threonine synthase; Validated
Probab=25.50 E-value=54 Score=21.44 Aligned_cols=26 Identities=31% Similarity=0.684 Sum_probs=16.8
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceeccccccccc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 52 (99)
+.|..||+.+.. ...+.|+.|+..+.
T Consensus 4 ~~C~~Cg~~~~~-------------~~~~~C~~cg~~l~ 29 (338)
T PRK06450 4 EVCMKCGKERES-------------IYEIRCKKCGGPFE 29 (338)
T ss_pred eEECCcCCcCCC-------------cccccCCcCCCEeE
Confidence 679999987632 12367887875443
No 234
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=25.49 E-value=48 Score=15.67 Aligned_cols=13 Identities=15% Similarity=0.278 Sum_probs=7.6
Q ss_pred CCCeecccCcCcC
Q psy16685 11 EKPHVCSVCSKGF 23 (99)
Q Consensus 11 ~~~~~C~~c~~~~ 23 (99)
...|.|+.||-.+
T Consensus 12 ~v~~~Cp~cGipt 24 (55)
T PF13824_consen 12 HVNFECPDCGIPT 24 (55)
T ss_pred ccCCcCCCCCCcC
Confidence 3456677776543
No 235
>PLN02748 tRNA dimethylallyltransferase
Probab=25.37 E-value=63 Score=22.39 Aligned_cols=24 Identities=17% Similarity=0.418 Sum_probs=15.3
Q ss_pred CCeecccCcC-cCCChHHHHHHhhh
Q psy16685 12 KPHVCSVCSK-GFSTSSSLNTHRRI 35 (99)
Q Consensus 12 ~~~~C~~c~~-~~~~~~~l~~h~~~ 35 (99)
+.|.|..|+. ++........|+..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 4566777776 56666666666553
No 236
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=25.36 E-value=35 Score=21.60 Aligned_cols=27 Identities=19% Similarity=0.527 Sum_probs=13.4
Q ss_pred ecccCcCcCCChHHHHHHhhhcCCCCceeccccc
Q psy16685 15 VCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCG 48 (99)
Q Consensus 15 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~ 48 (99)
.|+.||+-......+ .+.-.|+|..|.
T Consensus 222 ~CP~Cg~~W~L~~pl-------h~iFdFKCD~CR 248 (258)
T PF10071_consen 222 KCPSCGGDWRLKEPL-------HDIFDFKCDPCR 248 (258)
T ss_pred CCCCCCCccccCCch-------hhceeccCCcce
Confidence 466666555544433 122345666554
No 237
>PRK07591 threonine synthase; Validated
Probab=25.18 E-value=48 Score=22.39 Aligned_cols=28 Identities=21% Similarity=0.561 Sum_probs=18.2
Q ss_pred CeecccCcCcCCChHHHHHHhhhcCCCCceecccccccccC
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTA 53 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 53 (99)
-+.|..||..|.. ... |.|+.|+..+..
T Consensus 18 ~l~C~~Cg~~~~~------------~~~-~~C~~cg~~l~~ 45 (421)
T PRK07591 18 ALKCRECGAEYPL------------GPI-HVCEECFGPLEV 45 (421)
T ss_pred EEEeCCCCCcCCC------------CCC-ccCCCCCCeEEE
Confidence 4679999987752 122 788888755443
No 238
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=24.61 E-value=62 Score=19.13 Aligned_cols=19 Identities=21% Similarity=0.588 Sum_probs=14.4
Q ss_pred CCeecccCcCcCCChHHHH
Q psy16685 12 KPHVCSVCSKGFSTSSSLN 30 (99)
Q Consensus 12 ~~~~C~~c~~~~~~~~~l~ 30 (99)
....|..||+.|.....+.
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVA 131 (181)
T ss_pred ccCcCcccCCccCcHhHHH
Confidence 4667999999998765554
No 239
>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=24.29 E-value=29 Score=15.80 Aligned_cols=10 Identities=30% Similarity=0.966 Sum_probs=3.6
Q ss_pred Cceecccccc
Q psy16685 40 KPHQCQVCGK 49 (99)
Q Consensus 40 ~~~~C~~C~~ 49 (99)
..|.|+.|++
T Consensus 40 ~~W~CPiC~~ 49 (50)
T PF02891_consen 40 PKWKCPICNK 49 (50)
T ss_dssp ---B-TTT--
T ss_pred CCeECcCCcC
Confidence 3489998864
No 240
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=24.25 E-value=30 Score=22.91 Aligned_cols=12 Identities=25% Similarity=0.839 Sum_probs=7.9
Q ss_pred ceeccccccccc
Q psy16685 41 PHQCQVCGKRFT 52 (99)
Q Consensus 41 ~~~C~~C~~~f~ 52 (99)
.|.|+.||..+.
T Consensus 265 ~wrCpkCGg~ik 276 (403)
T COG1379 265 RWRCPKCGGKIK 276 (403)
T ss_pred cccCcccccchh
Confidence 367777777543
No 241
>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=24.20 E-value=33 Score=14.45 Aligned_cols=13 Identities=38% Similarity=0.733 Sum_probs=5.5
Q ss_pred eecccCcCcCCCh
Q psy16685 14 HVCSVCSKGFSTS 26 (99)
Q Consensus 14 ~~C~~c~~~~~~~ 26 (99)
-.|..|++.|..+
T Consensus 4 ~~C~eC~~~f~dS 16 (34)
T PF01286_consen 4 PKCDECGKPFMDS 16 (34)
T ss_dssp EE-TTT--EES-S
T ss_pred chHhHhCCHHHHH
Confidence 3577777776543
No 242
>KOG0402|consensus
Probab=24.17 E-value=23 Score=18.31 Aligned_cols=12 Identities=25% Similarity=0.506 Sum_probs=7.3
Q ss_pred Cceecccccccc
Q psy16685 40 KPHQCQVCGKRF 51 (99)
Q Consensus 40 ~~~~C~~C~~~f 51 (99)
..|.|..|.+.+
T Consensus 53 GiW~C~~C~kv~ 64 (92)
T KOG0402|consen 53 GIWKCGSCKKVV 64 (92)
T ss_pred eEEecCCcccee
Confidence 356777666544
No 243
>PRK05580 primosome assembly protein PriA; Validated
Probab=24.14 E-value=52 Score=23.81 Aligned_cols=11 Identities=36% Similarity=1.008 Sum_probs=6.8
Q ss_pred Cceeccccccc
Q psy16685 40 KPHQCQVCGKR 50 (99)
Q Consensus 40 ~~~~C~~C~~~ 50 (99)
.|+.|+.|+..
T Consensus 420 ~~~~Cp~Cg~~ 430 (679)
T PRK05580 420 IPKACPECGST 430 (679)
T ss_pred CCCCCCCCcCC
Confidence 45667777643
No 244
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=24.13 E-value=25 Score=22.70 Aligned_cols=32 Identities=25% Similarity=0.393 Sum_probs=19.6
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccccccccCc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTAS 54 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 54 (99)
.+|+.|+.....+. | ....+.|+.|+.-|.-.
T Consensus 39 ~kc~~C~~~~~~~~-l--------~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 39 VQCENCYGLNYKKF-L--------KSKMNICEQCGYHLKMS 70 (296)
T ss_pred eECCCccchhhHHH-H--------HHcCCCCCCCCCCcCCC
Confidence 45888876654332 1 12346899998876543
No 245
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=24.12 E-value=47 Score=22.80 Aligned_cols=13 Identities=23% Similarity=0.452 Sum_probs=9.6
Q ss_pred CCeecccCcCcCC
Q psy16685 12 KPHVCSVCSKGFS 24 (99)
Q Consensus 12 ~~~~C~~c~~~~~ 24 (99)
..|.|..||....
T Consensus 6 t~f~C~~CG~~s~ 18 (456)
T COG1066 6 TAFVCQECGYVSP 18 (456)
T ss_pred cEEEcccCCCCCc
Confidence 4588999986643
No 246
>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=24.01 E-value=26 Score=21.43 Aligned_cols=31 Identities=16% Similarity=0.103 Sum_probs=0.0
Q ss_pred CceecccccccccCcchHHHHHHhccCCCcch
Q psy16685 40 KPHQCQVCGKRFTASSNLYYHRMTHIKVNDDF 71 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~ 71 (99)
.-..|+.||..... +.+..|+++..-.-.|.
T Consensus 167 ~~~~cPitGe~IP~-~e~~eHmRi~LlDP~wk 197 (229)
T PF12230_consen 167 KMIICPITGEMIPA-DEMDEHMRIELLDPRWK 197 (229)
T ss_dssp --------------------------------
T ss_pred cccccccccccccc-ccccccccccccccccc
Confidence 44689999887643 45888998876543333
No 247
>KOG4727|consensus
Probab=23.97 E-value=49 Score=19.66 Aligned_cols=22 Identities=23% Similarity=0.317 Sum_probs=17.8
Q ss_pred CeecccCcCcCCChHHHHHHhh
Q psy16685 13 PHVCSVCSKGFSTSSSLNTHRR 34 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l~~h~~ 34 (99)
-|.|.+|.-++....++..|+-
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 5889999999988877776654
No 248
>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=23.73 E-value=38 Score=19.53 Aligned_cols=17 Identities=24% Similarity=0.468 Sum_probs=13.1
Q ss_pred CeecccCcCcCCChHHH
Q psy16685 13 PHVCSVCSKGFSTSSSL 29 (99)
Q Consensus 13 ~~~C~~c~~~~~~~~~l 29 (99)
.=.|..|++.|++-..+
T Consensus 28 RReC~~C~~RFTTyErv 44 (147)
T TIGR00244 28 RRECLECHERFTTFERA 44 (147)
T ss_pred cccCCccCCccceeeec
Confidence 34799999999876544
No 249
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=23.70 E-value=40 Score=13.78 Aligned_cols=12 Identities=25% Similarity=0.534 Sum_probs=8.7
Q ss_pred CCeecccCcCcC
Q psy16685 12 KPHVCSVCSKGF 23 (99)
Q Consensus 12 ~~~~C~~c~~~~ 23 (99)
+-|.|..||...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 357888888664
No 250
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=23.68 E-value=59 Score=22.43 Aligned_cols=25 Identities=24% Similarity=0.279 Sum_probs=21.2
Q ss_pred CceecccccccccCcchHHHHHHhc
Q psy16685 40 KPHQCQVCGKRFTASSNLYYHRMTH 64 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~~~l~~H~~~h 64 (99)
..|.|..|.+-|.....|.+|+...
T Consensus 197 ~lyiCe~Cl~y~~~~~~~~~H~~~C 221 (450)
T PLN00104 197 KLYFCEFCLKFMKRKEQLQRHMKKC 221 (450)
T ss_pred eEEEchhhhhhhcCHHHHHHHHhcC
Confidence 4589999999999999999998743
No 251
>PRK12722 transcriptional activator FlhC; Provisional
Probab=23.49 E-value=54 Score=19.73 Aligned_cols=32 Identities=16% Similarity=0.316 Sum_probs=19.6
Q ss_pred CceecccccccccCcchHHHHHHhccCCCcchhhhccccc
Q psy16685 40 KPHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNLEP 79 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~ 79 (99)
....|..|+..|..... .-...+.|..|.+..
T Consensus 133 ~l~~C~~Cgg~fv~~~~--------e~~~~f~CplC~~ps 164 (187)
T PRK12722 133 QLSSCNCCGGHFVTHAH--------DPVGSFVCGLCQPPS 164 (187)
T ss_pred eeccCCCCCCCeecccc--------ccCCCCcCCCCCCcc
Confidence 34568888877764432 224567777777643
No 252
>PRK00420 hypothetical protein; Validated
Probab=23.35 E-value=61 Score=17.76 Aligned_cols=13 Identities=31% Similarity=0.560 Sum_probs=8.4
Q ss_pred ceecccccccccC
Q psy16685 41 PHQCQVCGKRFTA 53 (99)
Q Consensus 41 ~~~C~~C~~~f~~ 53 (99)
...|+.||....-
T Consensus 40 ~~~Cp~Cg~~~~v 52 (112)
T PRK00420 40 EVVCPVHGKVYIV 52 (112)
T ss_pred ceECCCCCCeeee
Confidence 4678888775443
No 253
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=23.28 E-value=36 Score=16.07 Aligned_cols=10 Identities=20% Similarity=0.707 Sum_probs=6.4
Q ss_pred CeecccCcCc
Q psy16685 13 PHVCSVCSKG 22 (99)
Q Consensus 13 ~~~C~~c~~~ 22 (99)
-..|+.||..
T Consensus 4 Wi~CP~CgnK 13 (55)
T PF14205_consen 4 WILCPICGNK 13 (55)
T ss_pred EEECCCCCCc
Confidence 3468888753
No 254
>PRK12860 transcriptional activator FlhC; Provisional
Probab=23.04 E-value=54 Score=19.75 Aligned_cols=49 Identities=10% Similarity=0.095 Sum_probs=27.0
Q ss_pred CCChHHHHHHhhhcCCCCceecccccccccCcchHHHHHHhccCCCcchhhhcccccc
Q psy16685 23 FSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKEILNLEPV 80 (99)
Q Consensus 23 ~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~ 80 (99)
+.....|.+..... --....|..|+..|..... .....+.|..|.+...
T Consensus 117 ~tRAw~LvRf~~s~-~L~l~~C~~Cgg~fv~~~~--------e~~~~f~CplC~~psR 165 (189)
T PRK12860 117 LTRAWTLVRFFDAG-MLQLARCCRCGGKFVTHAH--------DLRHNFVCGLCQPPSR 165 (189)
T ss_pred HHHHHHHHHHhcCC-CeeeccCCCCCCCeecccc--------ccCCCCcCCCCCCccc
Confidence 33344455444422 1244678888888764422 3345677888875443
No 255
>KOG1994|consensus
Probab=23.01 E-value=66 Score=20.13 Aligned_cols=21 Identities=29% Similarity=0.738 Sum_probs=12.4
Q ss_pred CceecccccccccCcchHHHH
Q psy16685 40 KPHQCQVCGKRFTASSNLYYH 60 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~~~l~~H 60 (99)
..|=|-.||..|.+...|..|
T Consensus 238 eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 238 EHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred cceEEEEeccccCCHHHHHHh
Confidence 445566666666666665554
No 256
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=22.92 E-value=30 Score=16.37 Aligned_cols=11 Identities=27% Similarity=0.869 Sum_probs=3.5
Q ss_pred CCeecccCcCc
Q psy16685 12 KPHVCSVCSKG 22 (99)
Q Consensus 12 ~~~~C~~c~~~ 22 (99)
+.|.|+.||..
T Consensus 32 r~y~Cp~CgAt 42 (55)
T PF05741_consen 32 RKYVCPICGAT 42 (55)
T ss_dssp GG---TTT---
T ss_pred hcCcCCCCcCc
Confidence 45778888754
No 257
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.81 E-value=25 Score=16.14 Aligned_cols=11 Identities=36% Similarity=0.908 Sum_probs=8.4
Q ss_pred ecccccccccC
Q psy16685 43 QCQVCGKRFTA 53 (99)
Q Consensus 43 ~C~~C~~~f~~ 53 (99)
.|+.|++.|.-
T Consensus 14 ICpvCqRPFsW 24 (54)
T COG4338 14 ICPVCQRPFSW 24 (54)
T ss_pred hhhhhcCchHH
Confidence 58888888753
No 258
>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=22.73 E-value=42 Score=13.72 Aligned_cols=11 Identities=18% Similarity=0.528 Sum_probs=7.7
Q ss_pred CeecccCcCcC
Q psy16685 13 PHVCSVCSKGF 23 (99)
Q Consensus 13 ~~~C~~c~~~~ 23 (99)
-|.|..||...
T Consensus 4 ~ykC~~CGniv 14 (34)
T cd00974 4 VYKCEICGNIV 14 (34)
T ss_pred EEEcCCCCcEE
Confidence 47788887654
No 259
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=22.62 E-value=50 Score=14.33 Aligned_cols=10 Identities=30% Similarity=0.826 Sum_probs=6.5
Q ss_pred CeecccCcCc
Q psy16685 13 PHVCSVCSKG 22 (99)
Q Consensus 13 ~~~C~~c~~~ 22 (99)
|..|+.||..
T Consensus 2 ~~~Cp~Cg~~ 11 (47)
T PF14690_consen 2 PPRCPHCGSP 11 (47)
T ss_pred CccCCCcCCC
Confidence 5567788743
No 260
>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=22.51 E-value=40 Score=14.41 Aligned_cols=14 Identities=21% Similarity=0.698 Sum_probs=9.0
Q ss_pred CceecccccccccC
Q psy16685 40 KPHQCQVCGKRFTA 53 (99)
Q Consensus 40 ~~~~C~~C~~~f~~ 53 (99)
..+.|+.||..+.+
T Consensus 31 p~~~C~~CGE~~~~ 44 (46)
T TIGR03831 31 PALVCPQCGEEYLD 44 (46)
T ss_pred CccccccCCCEeeC
Confidence 34678888876543
No 261
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=22.51 E-value=15 Score=19.38 Aligned_cols=8 Identities=38% Similarity=1.165 Sum_probs=4.0
Q ss_pred eecccccc
Q psy16685 42 HQCQVCGK 49 (99)
Q Consensus 42 ~~C~~C~~ 49 (99)
..|+.||.
T Consensus 63 ~~Cp~Cg~ 70 (104)
T TIGR01384 63 VECPKCGH 70 (104)
T ss_pred CCCCCCCC
Confidence 35555553
No 262
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=22.47 E-value=49 Score=17.98 Aligned_cols=12 Identities=33% Similarity=0.822 Sum_probs=6.7
Q ss_pred CeecccCcCcCC
Q psy16685 13 PHVCSVCSKGFS 24 (99)
Q Consensus 13 ~~~C~~c~~~~~ 24 (99)
...|..|+..|.
T Consensus 54 ~~~C~~C~~~fg 65 (118)
T PF02318_consen 54 ERHCARCGKPFG 65 (118)
T ss_dssp CSB-TTTS-BCS
T ss_pred CcchhhhCCccc
Confidence 346888887764
No 263
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=22.06 E-value=36 Score=15.85 Aligned_cols=10 Identities=40% Similarity=1.072 Sum_probs=6.3
Q ss_pred eccccccccc
Q psy16685 43 QCQVCGKRFT 52 (99)
Q Consensus 43 ~C~~C~~~f~ 52 (99)
.|+.||..+.
T Consensus 2 ~CPyCge~~~ 11 (52)
T PF14255_consen 2 QCPYCGEPIE 11 (52)
T ss_pred CCCCCCCeeE
Confidence 5777776544
No 264
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=21.99 E-value=24 Score=22.74 Aligned_cols=10 Identities=40% Similarity=1.215 Sum_probs=6.6
Q ss_pred eecccccccc
Q psy16685 42 HQCQVCGKRF 51 (99)
Q Consensus 42 ~~C~~C~~~f 51 (99)
|.|..|+..+
T Consensus 287 ~~C~~Cg~~w 296 (299)
T TIGR01385 287 VTCEECGNRW 296 (299)
T ss_pred EEcCCCCCee
Confidence 5777777554
No 265
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=21.96 E-value=55 Score=15.05 Aligned_cols=17 Identities=29% Similarity=0.583 Sum_probs=10.7
Q ss_pred CCCceecccccccccCc
Q psy16685 38 GEKPHQCQVCGKRFTAS 54 (99)
Q Consensus 38 ~~~~~~C~~C~~~f~~~ 54 (99)
+.....|+.|+..|-..
T Consensus 37 ~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 37 GCNRVTCPKCGFSFCFR 53 (64)
T ss_pred CCCeeECCCCCCeECCC
Confidence 34556777777766543
No 266
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=21.89 E-value=38 Score=22.20 Aligned_cols=24 Identities=25% Similarity=0.722 Sum_probs=12.8
Q ss_pred ceecccccccccCcchHHHHHHhc
Q psy16685 41 PHQCQVCGKRFTASSNLYYHRMTH 64 (99)
Q Consensus 41 ~~~C~~C~~~f~~~~~l~~H~~~h 64 (99)
.|.|+.|...|......-.|...|
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHHHh
Confidence 455555555555555555554443
No 267
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=21.74 E-value=62 Score=20.39 Aligned_cols=38 Identities=21% Similarity=0.343 Sum_probs=19.8
Q ss_pred hcCCCCeecccCcCcCCChHHHHHHhhhcCCCCceecccccc
Q psy16685 8 LISEKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGK 49 (99)
Q Consensus 8 h~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 49 (99)
|-.-..+.|..|+..+........ .....+-.|+.|+.
T Consensus 117 HGsl~~~~C~~C~~~~~~~~~~~~----~~~~~~p~C~~Cg~ 154 (250)
T COG0846 117 HGSLKRVRCSKCGNQYYDEDVIKF----IEDGLIPRCPKCGG 154 (250)
T ss_pred ccceeeeEeCCCcCccchhhhhhh----cccCCCCcCccCCC
Confidence 333455678888777664331111 01113456777776
No 268
>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=21.73 E-value=21 Score=22.66 Aligned_cols=18 Identities=33% Similarity=0.741 Sum_probs=10.7
Q ss_pred CceecccccccccCcchH
Q psy16685 40 KPHQCQVCGKRFTASSNL 57 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~~~l 57 (99)
++++|+.|+........|
T Consensus 208 k~~PCPKCg~et~eTkdL 225 (314)
T PF06524_consen 208 KPIPCPKCGYETQETKDL 225 (314)
T ss_pred CCCCCCCCCCcccccccc
Confidence 567777777654444444
No 269
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=21.69 E-value=54 Score=14.03 Aligned_cols=11 Identities=45% Similarity=1.111 Sum_probs=6.4
Q ss_pred ecccCcCcCCC
Q psy16685 15 VCSVCSKGFST 25 (99)
Q Consensus 15 ~C~~c~~~~~~ 25 (99)
.|+.|++.|--
T Consensus 4 ~CprC~kg~Hw 14 (36)
T PF14787_consen 4 LCPRCGKGFHW 14 (36)
T ss_dssp C-TTTSSSCS-
T ss_pred cCcccCCCcch
Confidence 57888877643
No 270
>PTZ00064 histone acetyltransferase; Provisional
Probab=21.66 E-value=75 Score=22.39 Aligned_cols=25 Identities=24% Similarity=0.347 Sum_probs=21.2
Q ss_pred CceecccccccccCcchHHHHHHhc
Q psy16685 40 KPHQCQVCGKRFTASSNLYYHRMTH 64 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~~~l~~H~~~h 64 (99)
..|.|..|.+-|.....|.+|+...
T Consensus 279 ~LYICEfCLkY~~s~~~l~rH~~~C 303 (552)
T PTZ00064 279 TLHFCEYCLDFFCFEDELIRHLSRC 303 (552)
T ss_pred eEEEccchhhhhCCHHHHHHHHhcC
Confidence 4589999999999999999998743
No 271
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=21.64 E-value=1.2e+02 Score=18.33 Aligned_cols=39 Identities=21% Similarity=0.430 Sum_probs=19.1
Q ss_pred hcCCCCeecccCcCcCCChHHHHHHhhhcCCCCceecccccc
Q psy16685 8 LISEKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGK 49 (99)
Q Consensus 8 h~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 49 (99)
|-.-....|..|+..+.....+.. .........|+.|+.
T Consensus 90 HG~~~~~~C~~C~~~~~~~~~~~~---~~~~~~~p~C~~Cgg 128 (206)
T cd01410 90 HGNMFIEVCKSCGPEYVRDDVVET---RGDKETGRRCHACGG 128 (206)
T ss_pred cCCcCcccCCCCCCccchHHHHHH---hhcCCCCCcCCCCcC
Confidence 444455668778766654332211 111122345777764
No 272
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=21.16 E-value=74 Score=17.50 Aligned_cols=10 Identities=30% Similarity=0.657 Sum_probs=5.0
Q ss_pred CeecccCcCc
Q psy16685 13 PHVCSVCSKG 22 (99)
Q Consensus 13 ~~~C~~c~~~ 22 (99)
...|+.|++.
T Consensus 69 ~V~CP~C~K~ 78 (114)
T PF11023_consen 69 QVECPNCGKQ 78 (114)
T ss_pred eeECCCCCCh
Confidence 3445555543
No 273
>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=20.92 E-value=57 Score=14.10 Aligned_cols=29 Identities=17% Similarity=0.362 Sum_probs=14.9
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccccccc
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRF 51 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 51 (99)
+.|+.|+.... .......-+.|..||...
T Consensus 1 m~Cp~Cg~~~~---------~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 1 MKCPNCGSKEI---------VFDPERGELVCPNCGLVL 29 (43)
T ss_dssp ESBTTTSSSEE---------EEETTTTEEEETTT-BBE
T ss_pred CCCcCCcCCce---------EEcCCCCeEECCCCCCEe
Confidence 45777776431 111223446788887653
No 274
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=20.80 E-value=47 Score=17.17 Aligned_cols=12 Identities=25% Similarity=0.927 Sum_probs=7.5
Q ss_pred ecccccccccCc
Q psy16685 43 QCQVCGKRFTAS 54 (99)
Q Consensus 43 ~C~~C~~~f~~~ 54 (99)
.|+.||..|...
T Consensus 10 ~C~~CG~d~~~~ 21 (86)
T PF06170_consen 10 RCPHCGLDYSHA 21 (86)
T ss_pred cccccCCccccC
Confidence 577777665543
No 275
>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=20.65 E-value=94 Score=13.25 Aligned_cols=12 Identities=25% Similarity=0.584 Sum_probs=4.6
Q ss_pred CeecccCcCcCC
Q psy16685 13 PHVCSVCSKGFS 24 (99)
Q Consensus 13 ~~~C~~c~~~~~ 24 (99)
.|-|+.|...+.
T Consensus 3 ryyCdyC~~~~~ 14 (38)
T PF06220_consen 3 RYYCDYCKKYLT 14 (38)
T ss_dssp S-B-TTT--B-S
T ss_pred Ceecccccceec
Confidence 466777877663
No 276
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=20.60 E-value=42 Score=13.50 Aligned_cols=11 Identities=27% Similarity=0.821 Sum_probs=5.7
Q ss_pred CCceecccccc
Q psy16685 39 EKPHQCQVCGK 49 (99)
Q Consensus 39 ~~~~~C~~C~~ 49 (99)
+....|+.|+.
T Consensus 19 g~~r~C~~Cg~ 29 (32)
T PF09297_consen 19 GWARRCPSCGH 29 (32)
T ss_dssp SS-EEESSSS-
T ss_pred cCEeECCCCcC
Confidence 34556777764
No 277
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=20.20 E-value=46 Score=16.43 Aligned_cols=14 Identities=21% Similarity=0.712 Sum_probs=9.0
Q ss_pred CceecccccccccC
Q psy16685 40 KPHQCQVCGKRFTA 53 (99)
Q Consensus 40 ~~~~C~~C~~~f~~ 53 (99)
-...|..||.....
T Consensus 37 t~V~C~~CG~~l~~ 50 (67)
T COG2051 37 TVVTCLICGTTLAE 50 (67)
T ss_pred eEEEecccccEEEe
Confidence 35678888776543
No 278
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=20.12 E-value=32 Score=22.12 Aligned_cols=31 Identities=19% Similarity=0.558 Sum_probs=19.1
Q ss_pred eecccCcCcCCChHHHHHHhhhcCCCCceecccccccccC
Q psy16685 14 HVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTA 53 (99)
Q Consensus 14 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 53 (99)
..|+.|+.....+. |. ...+.|+.|+.-|.-
T Consensus 28 ~~c~~c~~~~~~~~-l~--------~~~~vc~~c~~h~rl 58 (292)
T PRK05654 28 TKCPSCGQVLYRKE-LE--------ANLNVCPKCGHHMRI 58 (292)
T ss_pred eECCCccchhhHHH-HH--------hcCCCCCCCCCCeeC
Confidence 45888886554332 11 224689999987753
No 279
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=20.10 E-value=66 Score=15.47 Aligned_cols=15 Identities=33% Similarity=0.782 Sum_probs=10.0
Q ss_pred CceecccccccccCc
Q psy16685 40 KPHQCQVCGKRFTAS 54 (99)
Q Consensus 40 ~~~~C~~C~~~f~~~ 54 (99)
-...|..|+.....+
T Consensus 29 t~V~C~~Cg~~L~~P 43 (59)
T PRK00415 29 TVVRCLVCGKTLAEP 43 (59)
T ss_pred cEEECcccCCCcccC
Confidence 456788888765443
Done!