Query psy11364
Match_columns 101
No_of_seqs 123 out of 1662
Neff 9.9
Searched_HMMs 46136
Date Fri Aug 16 16:30:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11364.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11364hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.8 4.6E-21 1E-25 121.9 2.9 76 24-100 187-263 (279)
2 KOG2462|consensus 99.7 8.5E-18 1.8E-22 107.1 1.7 76 23-101 160-236 (279)
3 KOG3623|consensus 99.6 2.3E-16 5E-21 111.3 -1.6 76 24-100 894-970 (1007)
4 KOG3576|consensus 99.5 8.8E-16 1.9E-20 94.6 -4.1 78 22-100 115-193 (267)
5 KOG3623|consensus 99.4 4.4E-14 9.6E-19 100.0 -1.7 78 23-100 239-329 (1007)
6 PHA02768 hypothetical protein; 99.2 3.6E-12 7.7E-17 63.5 1.9 43 54-97 6-48 (55)
7 PHA00733 hypothetical protein 99.1 2.2E-11 4.7E-16 71.3 0.7 78 22-100 38-119 (128)
8 PF13465 zf-H2C2_2: Zinc-finge 98.9 6.2E-10 1.3E-14 47.7 2.2 25 68-92 1-26 (26)
9 KOG1074|consensus 98.9 1.2E-10 2.6E-15 83.8 -0.0 80 21-101 602-689 (958)
10 KOG3576|consensus 98.9 2.9E-10 6.2E-15 70.5 0.6 76 24-100 145-232 (267)
11 KOG1074|consensus 98.8 9.1E-10 2E-14 79.4 1.4 49 52-100 604-653 (958)
12 KOG3608|consensus 98.6 1.5E-09 3.2E-14 72.2 -3.5 75 23-100 236-312 (467)
13 PHA00732 hypothetical protein 98.5 8.5E-08 1.8E-12 51.6 2.4 38 53-92 1-39 (79)
14 PHA00616 hypothetical protein 98.5 1.2E-07 2.6E-12 45.2 2.0 33 53-85 1-34 (44)
15 KOG3608|consensus 98.4 5E-08 1.1E-12 65.1 0.0 54 24-77 263-316 (467)
16 KOG3993|consensus 98.3 3E-08 6.5E-13 67.2 -2.6 76 24-100 267-376 (500)
17 PHA02768 hypothetical protein; 98.2 4.3E-08 9.4E-13 48.9 -2.7 44 24-70 5-48 (55)
18 PLN03086 PRLI-interacting fact 98.1 6.5E-07 1.4E-11 63.4 0.9 61 24-90 453-514 (567)
19 PHA00733 hypothetical protein 98.1 2.2E-06 4.8E-11 50.2 1.7 52 23-77 72-123 (128)
20 PLN03086 PRLI-interacting fact 98.0 4.3E-06 9.3E-11 59.4 2.6 69 23-94 477-555 (567)
21 PF00096 zf-C2H2: Zinc finger, 98.0 6.3E-06 1.4E-10 33.9 2.1 23 54-76 1-23 (23)
22 COG5189 SFP1 Putative transcri 97.9 4E-06 8.7E-11 55.5 1.2 51 51-101 347-419 (423)
23 PF00096 zf-C2H2: Zinc finger, 97.9 3.2E-06 7E-11 34.8 0.0 21 81-101 1-21 (23)
24 PF05605 zf-Di19: Drought indu 97.8 1.8E-05 3.9E-10 39.5 2.6 45 53-100 2-49 (54)
25 PF13912 zf-C2H2_6: C2H2-type 97.7 1.4E-05 3E-10 34.1 0.9 22 80-101 1-22 (27)
26 PHA00616 hypothetical protein 97.7 7.4E-06 1.6E-10 39.0 -0.3 22 80-101 1-22 (44)
27 PF13912 zf-C2H2_6: C2H2-type 97.5 6.2E-05 1.3E-09 32.0 1.3 25 53-77 1-25 (27)
28 PF13894 zf-C2H2_4: C2H2-type 97.4 0.00016 3.5E-09 29.4 2.3 23 54-76 1-23 (24)
29 PRK04860 hypothetical protein; 97.4 7.7E-05 1.7E-09 45.3 1.5 39 52-94 118-157 (160)
30 PHA00732 hypothetical protein 97.3 5.4E-05 1.2E-09 40.8 -0.1 48 24-77 1-48 (79)
31 PF09237 GAGA: GAGA factor; I 97.3 0.00082 1.8E-08 32.9 3.9 33 48-80 19-52 (54)
32 PF13894 zf-C2H2_4: C2H2-type 97.3 0.00012 2.5E-09 29.9 0.7 20 81-100 1-20 (24)
33 PF12756 zf-C2H2_2: C2H2 type 97.2 0.00012 2.6E-09 40.4 0.6 23 53-75 50-72 (100)
34 smart00355 ZnF_C2H2 zinc finge 97.1 0.00062 1.4E-08 28.0 2.2 24 54-77 1-24 (26)
35 smart00355 ZnF_C2H2 zinc finge 96.9 0.00034 7.5E-09 28.8 0.6 21 81-101 1-21 (26)
36 PF12171 zf-C2H2_jaz: Zinc-fin 96.8 0.0011 2.3E-08 28.2 1.9 21 81-101 2-22 (27)
37 KOG3993|consensus 96.8 0.00024 5.3E-09 48.8 -0.6 48 54-101 268-316 (500)
38 PF12874 zf-met: Zinc-finger o 96.7 0.00071 1.5E-08 28.1 0.7 20 81-100 1-20 (25)
39 PF05605 zf-Di19: Drought indu 96.6 0.00059 1.3E-08 34.0 0.2 50 24-76 2-52 (54)
40 PF12874 zf-met: Zinc-finger o 96.0 0.0049 1.1E-07 25.4 1.5 22 54-75 1-22 (25)
41 KOG1146|consensus 95.8 0.0041 8.8E-08 48.2 1.3 52 50-101 462-539 (1406)
42 PF09237 GAGA: GAGA factor; I 95.3 0.0068 1.5E-07 29.7 0.6 22 79-100 23-44 (54)
43 smart00451 ZnF_U1 U1-like zinc 95.1 0.014 3E-07 26.0 1.2 19 81-99 4-22 (35)
44 PF13909 zf-H2C2_5: C2H2-type 95.0 0.033 7.2E-07 22.6 2.2 22 54-76 1-22 (24)
45 PF13913 zf-C2HC_2: zinc-finge 94.5 0.017 3.7E-07 24.1 0.7 17 55-72 4-20 (25)
46 KOG2186|consensus 93.1 0.064 1.4E-06 34.9 1.7 38 54-92 4-41 (276)
47 KOG2893|consensus 93.0 0.039 8.4E-07 35.8 0.7 38 56-96 13-50 (341)
48 cd00350 rubredoxin_like Rubred 90.9 0.14 3E-06 22.7 1.0 8 80-87 17-24 (33)
49 PF12756 zf-C2H2_2: C2H2 type 90.8 0.28 6E-06 26.7 2.4 68 26-101 1-71 (100)
50 COG5189 SFP1 Putative transcri 90.5 0.071 1.5E-06 36.0 -0.2 52 23-74 348-419 (423)
51 PF09538 FYDLN_acid: Protein o 89.8 0.27 5.8E-06 28.1 1.8 30 25-66 10-39 (108)
52 COG5048 FOG: Zn-finger [Genera 89.6 0.22 4.7E-06 33.8 1.6 59 24-83 289-354 (467)
53 PRK00464 nrdR transcriptional 89.5 0.27 5.7E-06 29.9 1.7 43 26-69 2-44 (154)
54 COG2888 Predicted Zn-ribbon RN 88.7 0.28 6E-06 24.9 1.2 32 52-87 26-57 (61)
55 COG4049 Uncharacterized protei 86.2 0.56 1.2E-05 23.5 1.4 26 50-75 14-39 (65)
56 PRK04860 hypothetical protein; 85.4 0.087 1.9E-06 32.1 -2.0 38 23-65 118-155 (160)
57 PHA00626 hypothetical protein 85.4 0.8 1.7E-05 22.9 1.7 17 51-67 21-37 (59)
58 cd00729 rubredoxin_SM Rubredox 85.2 0.54 1.2E-05 21.0 1.0 8 80-87 18-25 (34)
59 TIGR02300 FYDLN_acid conserved 83.3 0.96 2.1E-05 26.5 1.8 30 25-66 10-39 (129)
60 TIGR00373 conserved hypothetic 80.9 1.1 2.3E-05 27.3 1.5 31 52-90 108-138 (158)
61 PRK06266 transcription initiat 80.9 1 2.2E-05 28.0 1.3 32 52-91 116-147 (178)
62 PF13719 zinc_ribbon_5: zinc-r 80.1 1.2 2.6E-05 20.2 1.2 9 54-62 26-34 (37)
63 PF13717 zinc_ribbon_4: zinc-r 79.8 1.5 3.2E-05 19.8 1.4 10 80-89 25-34 (36)
64 COG5048 FOG: Zn-finger [Genera 79.5 0.46 1E-05 32.2 -0.5 49 52-100 288-343 (467)
65 smart00531 TFIIE Transcription 79.1 1.4 3E-05 26.4 1.5 36 52-90 98-133 (147)
66 PRK14890 putative Zn-ribbon RN 78.8 0.96 2.1E-05 22.9 0.6 32 52-88 24-56 (59)
67 COG1592 Rubrerythrin [Energy p 78.6 1.1 2.3E-05 27.6 0.9 23 53-87 134-156 (166)
68 smart00659 RPOLCX RNA polymera 78.1 1.4 3E-05 20.9 1.0 8 80-87 19-26 (44)
69 TIGR02098 MJ0042_CXXC MJ0042 f 77.7 1.5 3.2E-05 19.8 1.1 9 54-62 26-34 (38)
70 PF09845 DUF2072: Zn-ribbon co 76.2 1.4 3.1E-05 26.0 1.0 15 53-67 1-15 (131)
71 smart00734 ZnF_Rad18 Rad18-lik 76.0 1.6 3.4E-05 18.2 0.8 8 83-90 4-11 (26)
72 COG0068 HypF Hydrogenase matur 73.1 2.1 4.6E-05 32.1 1.4 60 26-91 125-184 (750)
73 PF09986 DUF2225: Uncharacteri 72.7 1.5 3.2E-05 28.0 0.4 44 23-66 4-61 (214)
74 KOG2785|consensus 72.6 2.5 5.4E-05 29.4 1.5 22 79-100 67-88 (390)
75 PF01927 Mut7-C: Mut7-C RNAse 72.6 4.5 9.8E-05 24.2 2.5 20 52-71 123-142 (147)
76 COG1198 PriA Primosomal protei 72.3 4.3 9.2E-05 30.8 2.8 47 24-89 435-484 (730)
77 PRK09678 DNA-binding transcrip 72.1 2.6 5.6E-05 22.3 1.2 41 25-68 2-44 (72)
78 smart00614 ZnF_BED BED zinc fi 71.8 1.5 3.3E-05 21.1 0.3 13 54-66 19-31 (50)
79 COG3364 Zn-ribbon containing p 70.1 2.5 5.3E-05 23.9 0.9 12 54-65 3-14 (112)
80 PRK00398 rpoP DNA-directed RNA 69.9 0.94 2E-05 21.5 -0.7 10 25-34 4-13 (46)
81 PF10083 DUF2321: Uncharacteri 69.3 3.3 7.1E-05 25.2 1.4 19 50-68 65-83 (158)
82 PF12760 Zn_Tnp_IS1595: Transp 69.3 5 0.00011 19.0 1.8 29 23-61 17-45 (46)
83 KOG1146|consensus 68.1 2.7 5.8E-05 33.8 1.0 72 24-101 1260-1349(1406)
84 smart00440 ZnF_C2C2 C2C2 Zinc 68.1 4.1 8.8E-05 18.8 1.3 12 52-63 27-38 (40)
85 COG3357 Predicted transcriptio 67.9 1.7 3.7E-05 24.0 -0.0 12 53-64 58-69 (97)
86 TIGR00244 transcriptional regu 67.9 4.4 9.6E-05 24.4 1.7 16 54-69 29-44 (147)
87 PF02892 zf-BED: BED zinc fing 67.8 6.5 0.00014 18.2 2.1 23 51-73 14-40 (45)
88 COG1996 RPC10 DNA-directed RNA 66.9 1.9 4.1E-05 21.0 0.0 11 53-63 6-16 (49)
89 PF07754 DUF1610: Domain of un 66.4 2.7 5.9E-05 17.3 0.5 8 53-60 16-23 (24)
90 COG1997 RPL43A Ribosomal prote 65.6 1.8 3.9E-05 23.7 -0.2 10 54-63 54-63 (89)
91 PF14353 CpXC: CpXC protein 65.5 2.6 5.7E-05 24.4 0.5 10 26-35 3-12 (128)
92 PF04959 ARS2: Arsenite-resist 65.4 2.8 6.1E-05 26.9 0.6 21 80-100 77-97 (214)
93 COG1327 Predicted transcriptio 65.0 5.5 0.00012 24.2 1.8 16 53-68 28-43 (156)
94 KOG4167|consensus 64.2 2.3 4.9E-05 32.2 0.0 26 52-77 791-816 (907)
95 PF10571 UPF0547: Uncharacteri 63.8 5 0.00011 16.7 1.0 13 23-35 13-25 (26)
96 PF05443 ROS_MUCR: ROS/MUCR tr 62.6 5.9 0.00013 23.5 1.6 25 51-78 70-94 (132)
97 PLN02294 cytochrome c oxidase 62.4 3.6 7.8E-05 25.4 0.7 22 71-92 132-153 (174)
98 PF03604 DNA_RNApol_7kD: DNA d 62.0 3 6.5E-05 18.4 0.2 9 80-88 17-25 (32)
99 smart00834 CxxC_CXXC_SSSS Puta 61.9 3.3 7.2E-05 18.7 0.4 11 81-91 6-16 (41)
100 PF15269 zf-C2H2_7: Zinc-finge 61.0 3.9 8.4E-05 19.6 0.5 20 54-73 21-40 (54)
101 cd00924 Cyt_c_Oxidase_Vb Cytoc 60.2 3.9 8.5E-05 22.9 0.5 20 72-91 71-90 (97)
102 PF04959 ARS2: Arsenite-resist 59.4 9.5 0.00021 24.5 2.2 25 51-75 75-99 (214)
103 PF09723 Zn-ribbon_8: Zinc rib 58.6 3.9 8.4E-05 19.0 0.3 11 81-91 6-16 (42)
104 PF01096 TFIIS_C: Transcriptio 58.6 2.4 5.1E-05 19.5 -0.5 12 52-63 27-38 (39)
105 KOG2785|consensus 57.4 13 0.00027 26.1 2.6 50 52-101 165-241 (390)
106 cd00730 rubredoxin Rubredoxin; 56.7 19 0.00041 17.5 2.6 13 25-37 2-14 (50)
107 TIGR00595 priA primosomal prot 56.7 11 0.00025 27.2 2.5 10 52-61 239-248 (505)
108 PF10537 WAC_Acf1_DNA_bd: ATP- 56.0 21 0.00046 20.1 3.0 38 52-89 2-39 (102)
109 PF08790 zf-LYAR: LYAR-type C2 55.5 3.3 7.2E-05 17.7 -0.2 8 83-90 3-10 (28)
110 smart00154 ZnF_AN1 AN1-like Zi 52.2 7.1 0.00015 17.9 0.6 14 80-93 12-25 (39)
111 KOG2593|consensus 52.1 9.9 0.00021 27.0 1.5 18 79-96 127-144 (436)
112 TIGR02605 CxxC_CxxC_SSSS putat 51.6 6.1 0.00013 19.0 0.3 11 81-91 6-16 (52)
113 PRK04023 DNA polymerase II lar 51.4 21 0.00045 28.4 3.1 11 23-33 625-635 (1121)
114 KOG4173|consensus 51.4 6.3 0.00014 25.3 0.5 46 55-100 108-166 (253)
115 PF07282 OrfB_Zn_ribbon: Putat 51.3 18 0.0004 18.3 2.2 34 24-68 28-61 (69)
116 PHA02998 RNA polymerase subuni 51.0 9.9 0.00021 23.8 1.2 14 53-66 171-184 (195)
117 PF08274 PhnA_Zn_Ribbon: PhnA 50.9 7.1 0.00015 16.9 0.5 9 53-61 19-27 (30)
118 PF01428 zf-AN1: AN1-like Zinc 49.5 5 0.00011 18.7 -0.1 15 79-93 12-26 (43)
119 PRK00432 30S ribosomal protein 49.3 15 0.00032 17.9 1.5 10 53-62 37-46 (50)
120 PRK14873 primosome assembly pr 49.1 14 0.0003 27.8 2.0 46 24-89 383-431 (665)
121 PF01155 HypA: Hydrogenase exp 48.8 9.6 0.00021 21.8 0.9 26 53-89 70-95 (113)
122 PRK03824 hypA hydrogenase nick 48.3 5.8 0.00013 23.5 -0.0 14 52-65 69-82 (135)
123 TIGR01562 FdhE formate dehydro 47.0 22 0.00048 24.2 2.5 10 24-33 184-193 (305)
124 COG4306 Uncharacterized protei 46.1 19 0.0004 21.3 1.8 17 51-67 66-82 (160)
125 KOG2907|consensus 45.2 8.2 0.00018 22.2 0.3 37 54-92 75-114 (116)
126 COG1594 RPB9 DNA-directed RNA 44.6 13 0.00029 21.3 1.1 13 79-91 99-111 (113)
127 COG4530 Uncharacterized protei 44.5 15 0.00032 21.2 1.2 13 51-63 24-36 (129)
128 PF10013 DUF2256: Uncharacteri 43.5 13 0.00029 17.4 0.8 12 82-93 10-21 (42)
129 PTZ00255 60S ribosomal protein 43.4 4.3 9.3E-05 22.4 -1.0 10 54-63 55-64 (90)
130 PF09963 DUF2197: Uncharacteri 43.4 6.8 0.00015 19.7 -0.2 7 54-60 32-38 (56)
131 PF13451 zf-trcl: Probable zin 42.5 8.9 0.00019 18.7 0.1 15 79-93 3-17 (49)
132 PF10071 DUF2310: Zn-ribbon-co 42.4 34 0.00073 22.8 2.8 51 4-62 198-250 (258)
133 PF13878 zf-C2H2_3: zinc-finge 41.5 34 0.00074 15.7 2.0 24 54-77 14-39 (41)
134 PF11672 DUF3268: Protein of u 41.5 36 0.00078 19.3 2.5 37 24-60 2-38 (102)
135 PRK12496 hypothetical protein; 41.2 15 0.00033 22.4 1.0 29 52-91 126-154 (164)
136 COG3091 SprT Zn-dependent meta 41.2 12 0.00027 22.7 0.6 34 52-89 116-149 (156)
137 PF12013 DUF3505: Protein of u 41.1 31 0.00066 19.3 2.2 24 54-77 81-108 (109)
138 PTZ00043 cytochrome c oxidase 41.0 13 0.00028 24.2 0.7 18 75-92 176-193 (268)
139 KOG2071|consensus 40.9 19 0.00042 26.6 1.6 27 51-77 416-442 (579)
140 smart00661 RPOL9 RNA polymeras 40.4 36 0.00078 16.0 2.2 12 53-64 20-31 (52)
141 PRK05580 primosome assembly pr 40.4 29 0.00063 26.2 2.5 8 53-60 408-415 (679)
142 PRK12380 hydrogenase nickel in 40.1 14 0.0003 21.2 0.7 25 53-88 70-94 (113)
143 COG1656 Uncharacterized conser 39.4 30 0.00064 21.4 2.0 20 53-72 130-149 (165)
144 PF04423 Rad50_zn_hook: Rad50 39.2 11 0.00024 18.4 0.2 12 82-93 22-33 (54)
145 KOG3408|consensus 39.2 12 0.00025 21.9 0.3 23 51-73 55-77 (129)
146 TIGR00622 ssl1 transcription f 39.1 52 0.0011 19.0 2.9 12 80-91 81-92 (112)
147 PLN02748 tRNA dimethylallyltra 39.0 18 0.00038 26.1 1.2 22 79-100 417-439 (468)
148 PRK00564 hypA hydrogenase nick 37.9 16 0.00035 21.0 0.7 26 53-89 71-97 (117)
149 KOG2636|consensus 37.8 22 0.00047 25.6 1.4 25 75-99 395-421 (497)
150 PF02176 zf-TRAF: TRAF-type zi 37.5 17 0.00037 17.7 0.7 39 52-91 8-53 (60)
151 PF01215 COX5B: Cytochrome c o 37.0 9.9 0.00021 22.7 -0.2 18 74-91 106-123 (136)
152 PF10263 SprT-like: SprT-like 37.0 7.1 0.00015 23.2 -0.9 33 52-91 122-154 (157)
153 TIGR00280 L37a ribosomal prote 36.3 4.9 0.00011 22.2 -1.5 10 54-63 54-63 (91)
154 TIGR00143 hypF [NiFe] hydrogen 36.1 16 0.00034 27.8 0.6 59 26-90 92-150 (711)
155 PRK03564 formate dehydrogenase 36.1 42 0.00092 22.9 2.6 11 23-33 186-196 (309)
156 TIGR01206 lysW lysine biosynth 36.0 35 0.00075 16.9 1.6 10 25-34 3-12 (54)
157 TIGR01384 TFS_arch transcripti 35.3 25 0.00054 19.5 1.2 13 79-91 89-101 (104)
158 PRK05978 hypothetical protein; 34.5 37 0.0008 20.6 1.9 11 24-34 33-43 (148)
159 PF01363 FYVE: FYVE zinc finge 34.2 25 0.00054 17.8 1.1 12 52-63 24-35 (69)
160 KOG2482|consensus 34.1 27 0.00059 24.3 1.4 23 53-75 195-217 (423)
161 TIGR00100 hypA hydrogenase nic 33.5 21 0.00045 20.5 0.7 26 53-89 70-95 (115)
162 TIGR00515 accD acetyl-CoA carb 33.3 30 0.00065 23.3 1.5 30 54-91 27-56 (285)
163 PF01286 XPA_N: XPA protein N- 33.1 18 0.00038 16.2 0.3 11 82-92 5-15 (34)
164 PF14803 Nudix_N_2: Nudix N-te 32.9 16 0.00035 16.2 0.2 11 51-61 20-30 (34)
165 COG4888 Uncharacterized Zn rib 32.8 2.9 6.2E-05 23.6 -2.8 9 52-60 21-29 (104)
166 COG4957 Predicted transcriptio 32.5 21 0.00046 21.3 0.7 24 52-78 75-98 (148)
167 TIGR02159 PA_CoA_Oxy4 phenylac 32.2 15 0.00032 22.1 -0.0 9 25-33 106-114 (146)
168 KOG3497|consensus 32.1 22 0.00047 18.2 0.6 15 80-94 4-18 (69)
169 PF07975 C1_4: TFIIH C1-like d 31.7 7.2 0.00016 19.1 -1.2 27 51-77 19-45 (51)
170 KOG0717|consensus 31.1 23 0.0005 25.6 0.7 20 81-100 293-312 (508)
171 COG1675 TFA1 Transcription ini 30.8 44 0.00094 20.9 1.8 30 52-89 112-141 (176)
172 COG4338 Uncharacterized protei 30.6 16 0.00034 17.8 -0.1 12 82-93 14-25 (54)
173 COG3677 Transposase and inacti 30.1 22 0.00048 20.9 0.5 12 80-91 53-64 (129)
174 TIGR01385 TFSII transcription 30.1 44 0.00095 22.7 1.9 41 22-63 256-296 (299)
175 COG0675 Transposase and inacti 30.0 50 0.0011 21.8 2.2 32 23-70 308-339 (364)
176 PRK03681 hypA hydrogenase nick 29.6 25 0.00055 20.1 0.6 27 53-89 70-96 (114)
177 CHL00174 accD acetyl-CoA carbo 29.6 39 0.00085 22.9 1.6 32 53-92 38-69 (296)
178 PF01194 RNA_pol_N: RNA polyme 29.4 34 0.00074 17.4 1.0 14 80-93 4-17 (60)
179 TIGR00686 phnA alkylphosphonat 28.7 51 0.0011 18.9 1.7 12 24-35 19-30 (109)
180 cd00065 FYVE FYVE domain; Zinc 28.6 32 0.00069 16.5 0.8 27 26-65 4-30 (57)
181 PF04780 DUF629: Protein of un 28.6 52 0.0011 23.9 2.1 29 50-78 54-83 (466)
182 PRK03976 rpl37ae 50S ribosomal 28.5 8.6 0.00019 21.3 -1.3 10 54-63 55-64 (90)
183 PF06397 Desulfoferrod_N: Desu 28.1 23 0.00049 16.1 0.2 11 79-89 5-15 (36)
184 PF07503 zf-HYPF: HypF finger; 28.0 5.4 0.00012 17.9 -1.9 12 80-91 21-32 (35)
185 PF06524 NOA36: NOA36 protein; 27.7 20 0.00043 24.0 -0.0 11 79-89 208-218 (314)
186 KOG3507|consensus 27.0 36 0.00078 17.3 0.8 13 51-63 35-47 (62)
187 smart00064 FYVE Protein presen 26.9 36 0.00078 17.1 0.9 28 25-65 11-38 (68)
188 PF13453 zf-TFIIB: Transcripti 26.6 76 0.0017 14.3 2.2 20 52-71 18-37 (41)
189 PRK04351 hypothetical protein; 26.0 24 0.00052 21.3 0.1 35 52-93 111-145 (149)
190 PRK05654 acetyl-CoA carboxylas 25.8 46 0.001 22.5 1.4 30 54-91 28-57 (292)
191 PF13824 zf-Mss51: Zinc-finger 25.8 49 0.0011 16.5 1.2 12 51-62 12-23 (55)
192 PRK14559 putative protein seri 25.5 91 0.002 23.7 3.0 11 24-34 15-25 (645)
193 COG1773 Rubredoxin [Energy pro 25.0 31 0.00068 17.2 0.4 10 81-90 4-13 (55)
194 PF12156 ATPase-cat_bd: Putati 24.6 50 0.0011 17.9 1.2 35 26-63 2-36 (88)
195 PRK14714 DNA polymerase II lar 24.5 2E+02 0.0044 24.0 4.7 10 53-62 692-701 (1337)
196 PF11931 DUF3449: Domain of un 24.3 25 0.00055 22.3 0.0 9 79-87 100-108 (196)
197 PF10621 FpoO: F420H2 dehydrog 24.3 39 0.00084 19.5 0.7 60 27-89 4-69 (119)
198 PRK08222 hydrogenase 4 subunit 24.2 50 0.0011 20.5 1.3 18 79-96 113-130 (181)
199 KOG0978|consensus 24.1 35 0.00077 26.0 0.7 21 79-99 677-697 (698)
200 smart00731 SprT SprT homologue 24.0 30 0.00066 20.5 0.3 32 53-91 112-144 (146)
201 PF10276 zf-CHCC: Zinc-finger 23.9 27 0.00058 16.2 0.0 10 53-62 29-38 (40)
202 PRK10220 hypothetical protein; 23.3 1.1E+02 0.0025 17.6 2.5 14 24-37 20-33 (111)
203 PF14311 DUF4379: Domain of un 23.1 65 0.0014 15.6 1.4 15 53-67 28-42 (55)
204 PF14369 zf-RING_3: zinc-finge 22.6 49 0.0011 14.7 0.8 10 26-35 23-32 (35)
205 PF00301 Rubredoxin: Rubredoxi 22.6 33 0.00072 16.4 0.2 10 81-90 2-11 (47)
206 PF04606 Ogr_Delta: Ogr/Delta- 22.4 30 0.00064 16.4 0.0 8 27-34 2-9 (47)
207 KOG1280|consensus 22.3 78 0.0017 22.2 2.0 37 51-87 77-116 (381)
208 KOG0782|consensus 22.2 23 0.00049 26.6 -0.6 17 24-40 253-269 (1004)
209 PRK04016 DNA-directed RNA poly 21.7 42 0.00091 17.2 0.5 13 80-92 4-16 (62)
210 COG2331 Uncharacterized protei 21.6 29 0.00064 18.6 -0.1 11 80-90 12-22 (82)
211 KOG4124|consensus 21.3 18 0.00039 25.2 -1.1 21 79-99 397-417 (442)
212 PF05191 ADK_lid: Adenylate ki 21.2 34 0.00073 15.4 0.1 9 82-90 3-11 (36)
213 PF14690 zf-ISL3: zinc-finger 20.6 54 0.0012 15.0 0.8 10 80-89 2-11 (47)
214 PRK06260 threonine synthase; V 20.6 54 0.0012 22.9 1.0 25 25-62 4-28 (397)
215 PF12773 DZR: Double zinc ribb 20.5 98 0.0021 14.4 1.7 6 82-87 31-36 (50)
216 PF14787 zf-CCHC_5: GAG-polypr 20.0 50 0.0011 15.0 0.5 14 82-95 4-17 (36)
No 1
>KOG2462|consensus
Probab=99.82 E-value=4.6e-21 Score=121.90 Aligned_cols=76 Identities=25% Similarity=0.394 Sum_probs=73.6
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhCC-CCcccccCccccCChHHHhccc
Q psy11364 24 PLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVSRSRDALRKHD 100 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~-kp~~C~~C~k~f~~~~~l~~H~ 100 (101)
+++|.+||+.|..+.-|+.|.+.+. +|+||.|..|+++|..+++|+.||++|.+ |+|.|..|+|.|...+.|.+|.
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRTHT-GEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ 263 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRTHT-GEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHS 263 (279)
T ss_pred CcccccccccccchHHhhccccccc-CCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhh
Confidence 8999999999999999999999988 69999999999999999999999999999 9999999999999999999985
No 2
>KOG2462|consensus
Probab=99.68 E-value=8.5e-18 Score=107.15 Aligned_cols=76 Identities=24% Similarity=0.416 Sum_probs=67.1
Q ss_pred CCCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhCC-CCcccccCccccCChHHHhcccC
Q psy11364 23 SPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVSRSRDALRKHDK 101 (101)
Q Consensus 23 ~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~-kp~~C~~C~k~f~~~~~l~~H~~ 101 (101)
..+.|+.||+.+.....+..|++.+. -+++|..|||+|..+.-|+.|+|.|+| |||.|..|+|+|.-+++|..||+
T Consensus 160 ka~~C~~C~K~YvSmpALkMHirTH~---l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQ 236 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMPALKMHIRTHT---LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQ 236 (279)
T ss_pred ccccCCCCCceeeehHHHhhHhhccC---CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHH
Confidence 36778888888777777777877654 478999999999999999999999999 99999999999999999999974
No 3
>KOG3623|consensus
Probab=99.55 E-value=2.3e-16 Score=111.27 Aligned_cols=76 Identities=14% Similarity=0.235 Sum_probs=70.7
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhCC-CCcccccCccccCChHHHhccc
Q psy11364 24 PLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVSRSRDALRKHD 100 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~-kp~~C~~C~k~f~~~~~l~~H~ 100 (101)
.|.|+.|.+.|.-.++|..|.=-+. +.|||.|..|.|+|..+-.|..|+|+|.| |||.|+.|+|+|+...+..+||
T Consensus 894 myaCDqCDK~FqKqSSLaRHKYEHs-GqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 894 MYACDQCDKAFQKQSSLARHKYEHS-GQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cchHHHHHHHHHhhHHHHHhhhhhc-CCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 8999999999999999877755444 69999999999999999999999999999 9999999999999999999997
No 4
>KOG3576|consensus
Probab=99.46 E-value=8.8e-16 Score=94.62 Aligned_cols=78 Identities=21% Similarity=0.343 Sum_probs=69.4
Q ss_pred CCCCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhCC-CCcccccCccccCChHHHhccc
Q psy11364 22 TSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVSRSRDALRKHD 100 (101)
Q Consensus 22 ~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~-kp~~C~~C~k~f~~~~~l~~H~ 100 (101)
.+.+.|..||+.|.-+.-+..|..-+.. -+.|.|..|||.|.....|++|++.|+| +||+|..|+|+|.+.-+|..|+
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~-vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSD-VKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccH-HHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 3589999999999888777777776654 6679999999999999999999999999 9999999999999998887775
No 5
>KOG3623|consensus
Probab=99.36 E-value=4.4e-14 Score=100.00 Aligned_cols=78 Identities=14% Similarity=0.206 Sum_probs=62.9
Q ss_pred CCCCCCCCCCCCccCCCCCCCCCCC------------CCCCcceecccchhhcCCHHHHHHHHHhhCC-CCcccccCccc
Q psy11364 23 SPLSSSIPGSSKTKASGSGTTGGSS------------NHSKLFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHV 89 (101)
Q Consensus 23 ~~~~c~~c~~~~~~~~~~~~~~~~~------------~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~-kp~~C~~C~k~ 89 (101)
..+.|..|...|.....+..|..++ ....|.|+|.+|+|+|..+-.|+.|+|+|.| |||+|+.|+|+
T Consensus 239 ~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKR 318 (1007)
T KOG3623|consen 239 PNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKR 318 (1007)
T ss_pred CCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccc
Confidence 4788999999886555443221111 1123679999999999999999999999999 99999999999
Q ss_pred cCChHHHhccc
Q psy11364 90 SRSRDALRKHD 100 (101)
Q Consensus 90 f~~~~~l~~H~ 100 (101)
|+...+...||
T Consensus 319 FSHSGSySSHm 329 (1007)
T KOG3623|consen 319 FSHSGSYSSHM 329 (1007)
T ss_pred cccCCcccccc
Confidence 99999988886
No 6
>PHA02768 hypothetical protein; Provisional
Probab=99.24 E-value=3.6e-12 Score=63.50 Aligned_cols=43 Identities=19% Similarity=0.411 Sum_probs=40.5
Q ss_pred eecccchhhcCCHHHHHHHHHhhCCCCcccccCccccCChHHHh
Q psy11364 54 ATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRSRDALR 97 (101)
Q Consensus 54 ~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f~~~~~l~ 97 (101)
|.|+.||+.|....+|..|++.|+ +|+.|..|++.|.+.+.|+
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~-k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN-TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC-CcccCCcccceecccceeE
Confidence 789999999999999999999999 8999999999999888775
No 7
>PHA00733 hypothetical protein
Probab=99.09 E-value=2.2e-11 Score=71.29 Aligned_cols=78 Identities=14% Similarity=0.169 Sum_probs=62.8
Q ss_pred CCCCCCCCCCCCCccCCCCCCC----CCCCCCCCcceecccchhhcCCHHHHHHHHHhhCCCCcccccCccccCChHHHh
Q psy11364 22 TSPLSSSIPGSSKTKASGSGTT----GGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRSRDALR 97 (101)
Q Consensus 22 ~~~~~c~~c~~~~~~~~~~~~~----~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f~~~~~l~ 97 (101)
+.++.|.+|.+.+.....+..+ ........++|.|..|++.|.....|..|++.+. .+|.|..|++.|.....|.
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~-~~~~C~~CgK~F~~~~sL~ 116 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTE-HSKVCPVCGKEFRNTDSTL 116 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcCC-cCccCCCCCCccCCHHHHH
Confidence 3588899998887766555443 1123334789999999999999999999998764 6899999999999999999
Q ss_pred ccc
Q psy11364 98 KHD 100 (101)
Q Consensus 98 ~H~ 100 (101)
.|+
T Consensus 117 ~H~ 119 (128)
T PHA00733 117 DHV 119 (128)
T ss_pred HHH
Confidence 886
No 8
>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=98.95 E-value=6.2e-10 Score=47.74 Aligned_cols=25 Identities=40% Similarity=0.703 Sum_probs=22.8
Q ss_pred HHHHHHHhhCC-CCcccccCccccCC
Q psy11364 68 NLRVHMETHQN-AFYACSSCSHVSRS 92 (101)
Q Consensus 68 ~l~~h~~~h~~-kp~~C~~C~k~f~~ 92 (101)
+|..|+++|++ +||.|+.|+++|.+
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 47899999999 99999999999963
No 9
>KOG1074|consensus
Probab=98.95 E-value=1.2e-10 Score=83.79 Aligned_cols=80 Identities=20% Similarity=0.316 Sum_probs=65.5
Q ss_pred CCCCCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhCC-----CCcccc---cCccccCC
Q psy11364 21 LTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQN-----AFYACS---SCSHVSRS 92 (101)
Q Consensus 21 ~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~-----kp~~C~---~C~k~f~~ 92 (101)
.++|.+|.+|-+....++.|..|-+.+. ++|||+|..||++|.++.+|+.|+.+|-. .++.|+ +|.+.|..
T Consensus 602 ~TdPNqCiiC~rVlSC~saLqmHyrtHt-GERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn 680 (958)
T KOG1074|consen 602 RTDPNQCIICLRVLSCPSALQMHYRTHT-GERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTN 680 (958)
T ss_pred cCCccceeeeeecccchhhhhhhhhccc-CcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccc
Confidence 3568889999988888888888888877 58899999999999999999999888864 367788 88888888
Q ss_pred hHHHhcccC
Q psy11364 93 RDALRKHDK 101 (101)
Q Consensus 93 ~~~l~~H~~ 101 (101)
.-.|.+|++
T Consensus 681 ~V~lpQhIr 689 (958)
T KOG1074|consen 681 AVTLPQHIR 689 (958)
T ss_pred cccccceEE
Confidence 777777753
No 10
>KOG3576|consensus
Probab=98.91 E-value=2.9e-10 Score=70.53 Aligned_cols=76 Identities=16% Similarity=0.294 Sum_probs=63.8
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHH-hhC----------C-CCcccccCccccC
Q psy11364 24 PLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHME-THQ----------N-AFYACSSCSHVSR 91 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~-~h~----------~-kp~~C~~C~k~f~ 91 (101)
.+.|..||++|.+.-.+..|.+.+. +-+||+|..|+|+|.++..|..|.+ +|. . |-|.|+.||..-.
T Consensus 145 r~lct~cgkgfndtfdlkrh~rtht-gvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~ 223 (267)
T KOG3576|consen 145 RHLCTFCGKGFNDTFDLKRHTRTHT-GVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSE 223 (267)
T ss_pred HHHHhhccCcccchhhhhhhhcccc-CccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCC
Confidence 6789999999999999999999887 5899999999999999999999976 454 3 7899999998766
Q ss_pred ChHHHhccc
Q psy11364 92 SRDALRKHD 100 (101)
Q Consensus 92 ~~~~l~~H~ 100 (101)
....+..|+
T Consensus 224 ~~e~~~~h~ 232 (267)
T KOG3576|consen 224 RPEVYYLHL 232 (267)
T ss_pred ChhHHHHHH
Confidence 665554443
No 11
>KOG1074|consensus
Probab=98.85 E-value=9.1e-10 Score=79.45 Aligned_cols=49 Identities=24% Similarity=0.497 Sum_probs=46.7
Q ss_pred cceecccchhhcCCHHHHHHHHHhhCC-CCcccccCccccCChHHHhccc
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVSRSRDALRKHD 100 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~~-kp~~C~~C~k~f~~~~~l~~H~ 100 (101)
.|-.|..|.++...++.|+-|.|.|+| +||+|++||++|.++.+|..|+
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~ 653 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHM 653 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcc
Confidence 467899999999999999999999999 9999999999999999999986
No 12
>KOG3608|consensus
Probab=98.59 E-value=1.5e-09 Score=72.15 Aligned_cols=75 Identities=15% Similarity=0.177 Sum_probs=48.8
Q ss_pred CCCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHh-hCC-CCcccccCccccCChHHHhccc
Q psy11364 23 SPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMET-HQN-AFYACSSCSHVSRSRDALRKHD 100 (101)
Q Consensus 23 ~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~-h~~-kp~~C~~C~k~f~~~~~l~~H~ 100 (101)
.+|+|..|-+.|.++..+..|...+ -+-|+|+.|......++.|.+|++. |.. |||+|+.|++.|.+.+.|.+|.
T Consensus 236 n~fqC~~C~KrFaTeklL~~Hv~rH---vn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~ 312 (467)
T KOG3608|consen 236 NSFQCAQCFKRFATEKLLKSHVVRH---VNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHV 312 (467)
T ss_pred CchHHHHHHHHHhHHHHHHHHHHHh---hhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHH
Confidence 3566666666665555555444332 2346667777667777777777664 555 7888888888888888887774
No 13
>PHA00732 hypothetical protein
Probab=98.51 E-value=8.5e-08 Score=51.65 Aligned_cols=38 Identities=24% Similarity=0.600 Sum_probs=27.9
Q ss_pred ceecccchhhcCCHHHHHHHHHh-hCCCCcccccCccccCC
Q psy11364 53 FATCFVCGKQLSNQYNLRVHMET-HQNAFYACSSCSHVSRS 92 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h~~~-h~~kp~~C~~C~k~f~~ 92 (101)
||.|..|++.|.....|..|++. |. ++.|+.||+.|.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~~ 39 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYRR 39 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeCC
Confidence 46788888888888888888763 54 4568888888774
No 14
>PHA00616 hypothetical protein
Probab=98.46 E-value=1.2e-07 Score=45.17 Aligned_cols=33 Identities=12% Similarity=0.281 Sum_probs=30.8
Q ss_pred ceecccchhhcCCHHHHHHHHHhhCC-CCccccc
Q psy11364 53 FATCFVCGKQLSNQYNLRVHMETHQN-AFYACSS 85 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h~~~h~~-kp~~C~~ 85 (101)
||.|..||+.|.....+..|++.|++ +|+.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 58999999999999999999999999 9998875
No 15
>KOG3608|consensus
Probab=98.41 E-value=5e-08 Score=65.07 Aligned_cols=54 Identities=15% Similarity=0.134 Sum_probs=40.3
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhC
Q psy11364 24 PLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQ 77 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~ 77 (101)
.|.|+.|.-+-...+++..|.+..+...+||+|..|.+.+...+.|+.|..+|.
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 677777777777777777777666666777888888887777777777777766
No 16
>KOG3993|consensus
Probab=98.32 E-value=3e-08 Score=67.25 Aligned_cols=76 Identities=21% Similarity=0.298 Sum_probs=58.4
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhC--------C-C---------------
Q psy11364 24 PLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQ--------N-A--------------- 79 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~--------~-k--------------- 79 (101)
-|.|..|-..+-+.-.|.+|.=... -..-|.|.+|+|+|....+|..|.|+|- + .
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RI-V~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRI-VHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCee-EEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhc
Confidence 5677777777777767766642211 1234899999999999999999999984 1 2
Q ss_pred ----------CcccccCccccCChHHHhccc
Q psy11364 80 ----------FYACSSCSHVSRSRDALRKHD 100 (101)
Q Consensus 80 ----------p~~C~~C~k~f~~~~~l~~H~ 100 (101)
-|.|..|+|.|.+...|..|+
T Consensus 346 ~rsg~dss~gi~~C~~C~KkFrRqAYLrKHq 376 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQ 376 (500)
T ss_pred cccCCcccCceeecHHhhhhhHHHHHHHHhH
Confidence 378999999999999999984
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.22 E-value=4.3e-08 Score=48.89 Aligned_cols=44 Identities=14% Similarity=-0.074 Sum_probs=38.2
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHH
Q psy11364 24 PLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLR 70 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~ 70 (101)
.|.|+.||+.|...+.+..|.+++. ++++|..|++.|...+.|.
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 5899999999999999999998865 5889999999998776653
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.15 E-value=6.5e-07 Score=63.42 Aligned_cols=61 Identities=13% Similarity=0.188 Sum_probs=28.1
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhCC-CCcccccCcccc
Q psy11364 24 PLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVS 90 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~-kp~~C~~C~k~f 90 (101)
.+.|+.|++.|. .+.+..|..+.+ .++.|+ |++.+ .+..|..|+..|.. +|+.|..|++.+
T Consensus 453 H~~C~~Cgk~f~-~s~LekH~~~~H---kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 453 HVHCEKCGQAFQ-QGEMEKHMKVFH---EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMV 514 (567)
T ss_pred CccCCCCCCccc-hHHHHHHHHhcC---CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCcc
Confidence 445555555553 233333333321 344554 55432 33445555555554 555555555544
No 19
>PHA00733 hypothetical protein
Probab=98.05 E-value=2.2e-06 Score=50.24 Aligned_cols=52 Identities=17% Similarity=0.175 Sum_probs=44.4
Q ss_pred CCCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhC
Q psy11364 23 SPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQ 77 (101)
Q Consensus 23 ~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~ 77 (101)
.|+.|+.||+.|...+.+..|...+ ..++.|..|++.|.....|..|+....
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r~h---~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIRYT---EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHhcC---CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 4899999999999999888777653 346899999999999999999987543
No 20
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.00 E-value=4.3e-06 Score=59.39 Aligned_cols=69 Identities=17% Similarity=0.271 Sum_probs=53.8
Q ss_pred CCCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCC----------HHHHHHHHHhhCCCCcccccCccccCC
Q psy11364 23 SPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSN----------QYNLRVHMETHQNAFYACSSCSHVSRS 92 (101)
Q Consensus 23 ~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~----------~~~l~~h~~~h~~kp~~C~~C~k~f~~ 92 (101)
.++.|+ ||..+ ....+..|...+.. .+++.|..|++.+.. ...|..|......+++.|..||+.+..
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp-~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrl 553 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCP-LRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSVML 553 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCC-CCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCeeee
Confidence 478999 99755 45667778776654 789999999998852 357999998873399999999998876
Q ss_pred hH
Q psy11364 93 RD 94 (101)
Q Consensus 93 ~~ 94 (101)
+.
T Consensus 554 rd 555 (567)
T PLN03086 554 KE 555 (567)
T ss_pred hh
Confidence 53
No 21
>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=98.00 E-value=6.3e-06 Score=33.86 Aligned_cols=23 Identities=43% Similarity=0.868 Sum_probs=15.2
Q ss_pred eecccchhhcCCHHHHHHHHHhh
Q psy11364 54 ATCFVCGKQLSNQYNLRVHMETH 76 (101)
Q Consensus 54 ~~C~~c~~~~~~~~~l~~h~~~h 76 (101)
|.|+.|++.|..+..|..|++.|
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 45667777777777777776653
No 22
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.92 E-value=4e-06 Score=55.49 Aligned_cols=51 Identities=29% Similarity=0.503 Sum_probs=43.2
Q ss_pred Ccceecc--cchhhcCCHHHHHHHHHh-h------------------CC-CCcccccCccccCChHHHhcccC
Q psy11364 51 KLFATCF--VCGKQLSNQYNLRVHMET-H------------------QN-AFYACSSCSHVSRSRDALRKHDK 101 (101)
Q Consensus 51 ~~~~~C~--~c~~~~~~~~~l~~h~~~-h------------------~~-kp~~C~~C~k~f~~~~~l~~H~~ 101 (101)
++||+|+ .|.|.|.....|+-|+.. | .. |||+|++|+|++.....|..|++
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 5999996 599999999999999753 2 04 89999999999999999988863
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=97.86 E-value=3.2e-06 Score=34.77 Aligned_cols=21 Identities=29% Similarity=0.733 Sum_probs=19.3
Q ss_pred cccccCccccCChHHHhcccC
Q psy11364 81 YACSSCSHVSRSRDALRKHDK 101 (101)
Q Consensus 81 ~~C~~C~k~f~~~~~l~~H~~ 101 (101)
|.|+.|++.|.....|.+|++
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 689999999999999999974
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=97.84 E-value=1.8e-05 Score=39.52 Aligned_cols=45 Identities=33% Similarity=0.470 Sum_probs=33.8
Q ss_pred ceecccchhhcCCHHHHHHHHH-hhCC--CCcccccCccccCChHHHhccc
Q psy11364 53 FATCFVCGKQLSNQYNLRVHME-THQN--AFYACSSCSHVSRSRDALRKHD 100 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h~~-~h~~--kp~~C~~C~k~f~~~~~l~~H~ 100 (101)
.|.|+.|++ ......|..|.. .|.. +.+.|++|...+. .+|..|+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl 49 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHL 49 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHH
Confidence 478999999 556677889965 4665 6899999987644 3777775
No 25
>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=97.72 E-value=1.4e-05 Score=34.15 Aligned_cols=22 Identities=32% Similarity=0.682 Sum_probs=14.0
Q ss_pred CcccccCccccCChHHHhcccC
Q psy11364 80 FYACSSCSHVSRSRDALRKHDK 101 (101)
Q Consensus 80 p~~C~~C~k~f~~~~~l~~H~~ 101 (101)
||.|..|++.|.....|..|++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~ 22 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKR 22 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHC
T ss_pred CCCCCccCCccCChhHHHHHhH
Confidence 4566666666666666666653
No 26
>PHA00616 hypothetical protein
Probab=97.68 E-value=7.4e-06 Score=39.05 Aligned_cols=22 Identities=23% Similarity=0.572 Sum_probs=20.4
Q ss_pred CcccccCccccCChHHHhcccC
Q psy11364 80 FYACSSCSHVSRSRDALRKHDK 101 (101)
Q Consensus 80 p~~C~~C~k~f~~~~~l~~H~~ 101 (101)
||.|+.||+.|...++|.+|++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r 22 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLL 22 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHH
Confidence 7999999999999999999974
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=97.48 E-value=6.2e-05 Score=32.03 Aligned_cols=25 Identities=36% Similarity=0.513 Sum_probs=22.5
Q ss_pred ceecccchhhcCCHHHHHHHHHhhC
Q psy11364 53 FATCFVCGKQLSNQYNLRVHMETHQ 77 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h~~~h~ 77 (101)
+|.|..|++.|.....|..|++.|.
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 5899999999999999999997664
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.44 E-value=0.00016 Score=29.45 Aligned_cols=23 Identities=43% Similarity=0.863 Sum_probs=14.8
Q ss_pred eecccchhhcCCHHHHHHHHHhh
Q psy11364 54 ATCFVCGKQLSNQYNLRVHMETH 76 (101)
Q Consensus 54 ~~C~~c~~~~~~~~~l~~h~~~h 76 (101)
|.|+.|++.|.....+..|+..|
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 46777777777777777777654
No 29
>PRK04860 hypothetical protein; Provisional
Probab=97.41 E-value=7.7e-05 Score=45.32 Aligned_cols=39 Identities=23% Similarity=0.494 Sum_probs=33.0
Q ss_pred cceecccchhhcCCHHHHHHHHHhhCC-CCcccccCccccCChH
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVSRSRD 94 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~~-kp~~C~~C~k~f~~~~ 94 (101)
-+|.|. |++ ....+.+|.++|++ ++|.|..|++.|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 468997 987 56678899999999 9999999999887543
No 30
>PHA00732 hypothetical protein
Probab=97.29 E-value=5.4e-05 Score=40.78 Aligned_cols=48 Identities=17% Similarity=0.270 Sum_probs=37.0
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhC
Q psy11364 24 PLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQ 77 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~ 77 (101)
|+.|..||+.|...+.+..|...... ++.|..|++.|.. +..|.....
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~---l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR---LNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC---hhhhhcccC
Confidence 57899999999999998888763221 3579999999984 778875544
No 31
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.27 E-value=0.00082 Score=32.93 Aligned_cols=33 Identities=33% Similarity=0.511 Sum_probs=22.8
Q ss_pred CCCCcceecccchhhcCCHHHHHHHHHhhCC-CC
Q psy11364 48 NHSKLFATCFVCGKQLSNQYNLRVHMETHQN-AF 80 (101)
Q Consensus 48 ~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~-kp 80 (101)
...+.|..|+.|+..+.+..+|.+|+.++.+ ||
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 3346789999999999999999999987766 65
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=97.25 E-value=0.00012 Score=29.90 Aligned_cols=20 Identities=35% Similarity=0.783 Sum_probs=16.7
Q ss_pred cccccCccccCChHHHhccc
Q psy11364 81 YACSSCSHVSRSRDALRKHD 100 (101)
Q Consensus 81 ~~C~~C~k~f~~~~~l~~H~ 100 (101)
|.|+.|++.|.....|..|+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~ 20 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHM 20 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHH
Confidence 67999999999999999996
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.18 E-value=0.00012 Score=40.37 Aligned_cols=23 Identities=26% Similarity=0.485 Sum_probs=12.9
Q ss_pred ceecccchhhcCCHHHHHHHHHh
Q psy11364 53 FATCFVCGKQLSNQYNLRVHMET 75 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h~~~ 75 (101)
.+.|..|++.|.....|..|++.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 35566666666666666666554
No 34
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.08 E-value=0.00062 Score=27.98 Aligned_cols=24 Identities=38% Similarity=0.688 Sum_probs=17.8
Q ss_pred eecccchhhcCCHHHHHHHHHhhC
Q psy11364 54 ATCFVCGKQLSNQYNLRVHMETHQ 77 (101)
Q Consensus 54 ~~C~~c~~~~~~~~~l~~h~~~h~ 77 (101)
|.|..|++.|.....+..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 457778888888888888877554
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.91 E-value=0.00034 Score=28.81 Aligned_cols=21 Identities=38% Similarity=0.896 Sum_probs=18.7
Q ss_pred cccccCccccCChHHHhcccC
Q psy11364 81 YACSSCSHVSRSRDALRKHDK 101 (101)
Q Consensus 81 ~~C~~C~k~f~~~~~l~~H~~ 101 (101)
|.|..|++.|.....|..|++
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 579999999999999998863
No 36
>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=96.85 E-value=0.0011 Score=28.19 Aligned_cols=21 Identities=29% Similarity=0.691 Sum_probs=16.7
Q ss_pred cccccCccccCChHHHhcccC
Q psy11364 81 YACSSCSHVSRSRDALRKHDK 101 (101)
Q Consensus 81 ~~C~~C~k~f~~~~~l~~H~~ 101 (101)
|-|..|++.|.....+..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 568888888888888888864
No 37
>KOG3993|consensus
Probab=96.77 E-value=0.00024 Score=48.82 Aligned_cols=48 Identities=21% Similarity=0.465 Sum_probs=41.9
Q ss_pred eecccchhhcCCHHHHHHHHHhhCC-CCcccccCccccCChHHHhcccC
Q psy11364 54 ATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVSRSRDALRKHDK 101 (101)
Q Consensus 54 ~~C~~c~~~~~~~~~l~~h~~~h~~-kp~~C~~C~k~f~~~~~l~~H~~ 101 (101)
|.|..|...|.....|.+|.-.--. .-|+|++|+|.|.-..+|..|.|
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRR 316 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRR 316 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhc
Confidence 7899999999999999999754444 57999999999999999988875
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.69 E-value=0.00071 Score=28.07 Aligned_cols=20 Identities=30% Similarity=0.670 Sum_probs=11.6
Q ss_pred cccccCccccCChHHHhccc
Q psy11364 81 YACSSCSHVSRSRDALRKHD 100 (101)
Q Consensus 81 ~~C~~C~k~f~~~~~l~~H~ 100 (101)
|.|.+|++.|.....+..|+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHL 20 (25)
T ss_dssp EEETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCCCcCCHHHHHHHH
Confidence 34556666666666665554
No 39
>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=96.59 E-value=0.00059 Score=33.99 Aligned_cols=50 Identities=14% Similarity=0.251 Sum_probs=33.6
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCC-CCCcceecccchhhcCCHHHHHHHHHhh
Q psy11364 24 PLSSSIPGSSKTKASGSGTTGGSSN-HSKLFATCFVCGKQLSNQYNLRVHMETH 76 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~~~~~~~~~~-~~~~~~~C~~c~~~~~~~~~l~~h~~~h 76 (101)
.|.|+.||+.+. ...|..|....+ ...+.+.|+.|...+. .++..|+..+
T Consensus 2 ~f~CP~C~~~~~-~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 2 SFTCPYCGKGFS-ESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred CcCCCCCCCccC-HHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 578999999544 455655543332 2345689999997644 4888888754
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.02 E-value=0.0049 Score=25.41 Aligned_cols=22 Identities=32% Similarity=0.688 Sum_probs=19.8
Q ss_pred eecccchhhcCCHHHHHHHHHh
Q psy11364 54 ATCFVCGKQLSNQYNLRVHMET 75 (101)
Q Consensus 54 ~~C~~c~~~~~~~~~l~~h~~~ 75 (101)
|.|..|++.|..+..+..|++.
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 6799999999999999999864
No 41
>KOG1146|consensus
Probab=95.83 E-value=0.0041 Score=48.25 Aligned_cols=52 Identities=23% Similarity=0.366 Sum_probs=45.2
Q ss_pred CCcceecccchhhcCCHHHHHHHHHh-hC------------------------C-CCcccccCccccCChHHHhcccC
Q psy11364 50 SKLFATCFVCGKQLSNQYNLRVHMET-HQ------------------------N-AFYACSSCSHVSRSRDALRKHDK 101 (101)
Q Consensus 50 ~~~~~~C~~c~~~~~~~~~l~~h~~~-h~------------------------~-kp~~C~~C~k~f~~~~~l~~H~~ 101 (101)
..+.+.|+.|+..|.....|..|+|. |. + +||.|..|...+....+|..|++
T Consensus 462 ~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 462 FFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 35779999999999999999999997 11 3 79999999999999999998863
No 42
>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=95.34 E-value=0.0068 Score=29.73 Aligned_cols=22 Identities=32% Similarity=0.526 Sum_probs=16.3
Q ss_pred CCcccccCccccCChHHHhccc
Q psy11364 79 AFYACSSCSHVSRSRDALRKHD 100 (101)
Q Consensus 79 kp~~C~~C~k~f~~~~~l~~H~ 100 (101)
.|..|++|+..+.+..+|.+|+
T Consensus 23 ~PatCP~C~a~~~~srnLrRHl 44 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHL 44 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHH
T ss_pred CCCCCCcchhhccchhhHHHHH
Confidence 7999999999999999999996
No 43
>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=95.05 E-value=0.014 Score=26.01 Aligned_cols=19 Identities=16% Similarity=0.454 Sum_probs=9.1
Q ss_pred cccccCccccCChHHHhcc
Q psy11364 81 YACSSCSHVSRSRDALRKH 99 (101)
Q Consensus 81 ~~C~~C~k~f~~~~~l~~H 99 (101)
|-|+.|++.|.....+..|
T Consensus 4 ~~C~~C~~~~~~~~~~~~H 22 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAH 22 (35)
T ss_pred eEccccCCccCCHHHHHHH
Confidence 4455555555544444444
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.98 E-value=0.033 Score=22.65 Aligned_cols=22 Identities=32% Similarity=0.582 Sum_probs=15.0
Q ss_pred eecccchhhcCCHHHHHHHHHhh
Q psy11364 54 ATCFVCGKQLSNQYNLRVHMETH 76 (101)
Q Consensus 54 ~~C~~c~~~~~~~~~l~~h~~~h 76 (101)
|.|..|..... +..|..|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 56888887776 77888887764
No 45
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.52 E-value=0.017 Score=24.10 Aligned_cols=17 Identities=35% Similarity=0.882 Sum_probs=7.9
Q ss_pred ecccchhhcCCHHHHHHH
Q psy11364 55 TCFVCGKQLSNQYNLRVH 72 (101)
Q Consensus 55 ~C~~c~~~~~~~~~l~~h 72 (101)
.|+.|++.| ....|..|
T Consensus 4 ~C~~CgR~F-~~~~l~~H 20 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKH 20 (25)
T ss_pred cCCCCCCEE-CHHHHHHH
Confidence 355555555 33334444
No 46
>KOG2186|consensus
Probab=93.06 E-value=0.064 Score=34.92 Aligned_cols=38 Identities=29% Similarity=0.710 Sum_probs=18.0
Q ss_pred eecccchhhcCCHHHHHHHHHhhCCCCcccccCccccCC
Q psy11364 54 ATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRS 92 (101)
Q Consensus 54 ~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f~~ 92 (101)
|.|..||....-+. +..|+....+.-|.|.-|++.|..
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCrn~~fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCRNAYFSCIDCGKTFER 41 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhccCCeeEEeeccccccc
Confidence 44555554443332 334554444444555555555554
No 47
>KOG2893|consensus
Probab=93.03 E-value=0.039 Score=35.78 Aligned_cols=38 Identities=21% Similarity=0.547 Sum_probs=28.3
Q ss_pred cccchhhcCCHHHHHHHHHhhCCCCcccccCccccCChHHH
Q psy11364 56 CFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRSRDAL 96 (101)
Q Consensus 56 C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f~~~~~l 96 (101)
|..|++.|....-|..|++. |.|+|-+|.|..-.-..|
T Consensus 13 cwycnrefddekiliqhqka---khfkchichkkl~sgpgl 50 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA---KHFKCHICHKKLFSGPGL 50 (341)
T ss_pred eeecccccchhhhhhhhhhh---ccceeeeehhhhccCCCc
Confidence 67889999998888877654 778999998765444333
No 48
>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=90.94 E-value=0.14 Score=22.74 Aligned_cols=8 Identities=25% Similarity=0.966 Sum_probs=4.3
Q ss_pred CcccccCc
Q psy11364 80 FYACSSCS 87 (101)
Q Consensus 80 p~~C~~C~ 87 (101)
|+.|++||
T Consensus 17 ~~~CP~Cg 24 (33)
T cd00350 17 PWVCPVCG 24 (33)
T ss_pred CCcCcCCC
Confidence 45555554
No 49
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=90.80 E-value=0.28 Score=26.66 Aligned_cols=68 Identities=18% Similarity=0.203 Sum_probs=18.3
Q ss_pred CCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHH---hhCCCCcccccCccccCChHHHhcccC
Q psy11364 26 SSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHME---THQNAFYACSSCSHVSRSRDALRKHDK 101 (101)
Q Consensus 26 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~---~h~~kp~~C~~C~k~f~~~~~l~~H~~ 101 (101)
+|..|+..|.....+..|....+.-..+ .. ..+.....+..+.+ ... +.|..|++.|.....|..|++
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~-~~----~~l~~~~~~~~~~~~~~~~~---~~C~~C~~~f~s~~~l~~Hm~ 71 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP-DQ----KYLVDPNRLLNYLRKKVKES---FRCPYCNKTFRSREALQEHMR 71 (100)
T ss_dssp -----------------------------------------------------SS---EEBSSSS-EESSHHHHHHHHH
T ss_pred Cccccccccccccccccccccccccccc-cc----cccccccccccccccccCCC---CCCCccCCCCcCHHHHHHHHc
Confidence 4888999998888887776544321111 00 00111111111111 113 479999999999999999873
No 50
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=90.52 E-value=0.071 Score=35.97 Aligned_cols=52 Identities=17% Similarity=0.236 Sum_probs=34.0
Q ss_pred CCCCCCC--CCCCCccCCCCCC-----CCC-------------CCCCCCcceecccchhhcCCHHHHHHHHH
Q psy11364 23 SPLSSSI--PGSSKTKASGSGT-----TGG-------------SSNHSKLFATCFVCGKQLSNQYNLRVHME 74 (101)
Q Consensus 23 ~~~~c~~--c~~~~~~~~~~~~-----~~~-------------~~~~~~~~~~C~~c~~~~~~~~~l~~h~~ 74 (101)
.||.|++ |.+.+...-.|.- |.. +-....+||.|++|+|.|..--.|+-|+.
T Consensus 348 KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred ceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 4899987 6666655544431 100 01112489999999999999888877753
No 51
>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=89.78 E-value=0.27 Score=28.08 Aligned_cols=30 Identities=17% Similarity=0.229 Sum_probs=17.1
Q ss_pred CCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCH
Q psy11364 25 LSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQ 66 (101)
Q Consensus 25 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~ 66 (101)
..|+.||+.|.. | ++.|..|+.||..|...
T Consensus 10 R~Cp~CG~kFYD---L---------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD---L---------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc---C---------CCCCccCCCCCCccCcc
Confidence 456666766632 1 23555667777666554
No 52
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.58 E-value=0.22 Score=33.79 Aligned_cols=59 Identities=20% Similarity=0.214 Sum_probs=36.9
Q ss_pred CCCCCCCCCCCccCCCCCCCCC--CCCCCC--cceecc--cchhhcCCHHHHHHHHHhhCC-CCccc
Q psy11364 24 PLSSSIPGSSKTKASGSGTTGG--SSNHSK--LFATCF--VCGKQLSNQYNLRVHMETHQN-AFYAC 83 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~~~~~~~--~~~~~~--~~~~C~--~c~~~~~~~~~l~~h~~~h~~-kp~~C 83 (101)
+..|..|...+.....+..+.. .+. .+ +++.|. .|++.+.....+..|...|++ .++.+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~-~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHS-GESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred CCCCccccCCccccccccccccccccc-cccCCceeeeccCCCccccccccccCCcccccCCCcccc
Confidence 4556666666666666666665 333 34 666666 577777777777777666666 54544
No 53
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=89.45 E-value=0.27 Score=29.87 Aligned_cols=43 Identities=16% Similarity=0.334 Sum_probs=22.3
Q ss_pred CCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHH
Q psy11364 26 SSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNL 69 (101)
Q Consensus 26 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l 69 (101)
.||.||.....--........... .+.+.|+.||..|.....+
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~-~~~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAI-RRRRECLACGKRFTTFERV 44 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCce-eeeeeccccCCcceEeEec
Confidence 588888755332221111111111 2337888888887765543
No 54
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=88.69 E-value=0.28 Score=24.86 Aligned_cols=32 Identities=19% Similarity=0.378 Sum_probs=20.0
Q ss_pred cceecccchhhcCCHHHHHHHHHhhCCCCcccccCc
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCS 87 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~ 87 (101)
-.|.|+.||++.-.+..-= --.+.+|.|+.||
T Consensus 26 v~F~CPnCGe~~I~Rc~~C----Rk~g~~Y~Cp~CG 57 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAKC----RKLGNPYRCPKCG 57 (61)
T ss_pred eEeeCCCCCceeeehhhhH----HHcCCceECCCcC
Confidence 4488999996544433211 1123799999998
No 55
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=86.20 E-value=0.56 Score=23.49 Aligned_cols=26 Identities=19% Similarity=0.427 Sum_probs=22.8
Q ss_pred CCcceecccchhhcCCHHHHHHHHHh
Q psy11364 50 SKLFATCFVCGKQLSNQYNLRVHMET 75 (101)
Q Consensus 50 ~~~~~~C~~c~~~~~~~~~l~~h~~~ 75 (101)
++..+.|+.|+..|.....+.+|...
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhH
Confidence 57778999999999999999999764
No 56
>PRK04860 hypothetical protein; Provisional
Probab=85.41 E-value=0.087 Score=32.13 Aligned_cols=38 Identities=13% Similarity=0.150 Sum_probs=28.3
Q ss_pred CCCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCC
Q psy11364 23 SPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSN 65 (101)
Q Consensus 23 ~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~ 65 (101)
.+|.|. |+. ....+..|.+++. ++++|.|..|+..+..
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~-g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVR-GEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhc-CCccEECCCCCceeEE
Confidence 478997 887 4455556777766 4788999999987754
No 57
>PHA00626 hypothetical protein
Probab=85.38 E-value=0.8 Score=22.94 Aligned_cols=17 Identities=24% Similarity=0.229 Sum_probs=11.8
Q ss_pred CcceecccchhhcCCHH
Q psy11364 51 KLFATCFVCGKQLSNQY 67 (101)
Q Consensus 51 ~~~~~C~~c~~~~~~~~ 67 (101)
...|.|..||..|+...
T Consensus 21 snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 21 SDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CcceEcCCCCCeechhh
Confidence 35588888887776544
No 58
>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=85.17 E-value=0.54 Score=21.00 Aligned_cols=8 Identities=25% Similarity=0.630 Sum_probs=4.5
Q ss_pred CcccccCc
Q psy11364 80 FYACSSCS 87 (101)
Q Consensus 80 p~~C~~C~ 87 (101)
|..|++||
T Consensus 18 p~~CP~Cg 25 (34)
T cd00729 18 PEKCPICG 25 (34)
T ss_pred CCcCcCCC
Confidence 45555555
No 59
>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=83.35 E-value=0.96 Score=26.54 Aligned_cols=30 Identities=17% Similarity=0.050 Sum_probs=17.5
Q ss_pred CCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCH
Q psy11364 25 LSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQ 66 (101)
Q Consensus 25 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~ 66 (101)
..|+.||+.|.. | ++.|..|+.||..|...
T Consensus 10 r~Cp~cg~kFYD---L---------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYD---L---------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccc---c---------CCCCccCCCcCCccCcc
Confidence 456777766633 1 23556677777666544
No 60
>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=80.95 E-value=1.1 Score=27.28 Aligned_cols=31 Identities=13% Similarity=0.370 Sum_probs=20.6
Q ss_pred cceecccchhhcCCHHHHHHHHHhhCCCCcccccCcccc
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVS 90 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f 90 (101)
.-|.|+.|+..|+....+. --|.|+.||...
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME--------LNFTCPRCGAML 138 (158)
T ss_pred CeEECCCCCcEeeHHHHHH--------cCCcCCCCCCEe
Confidence 4467777777777666654 257788887653
No 61
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=80.89 E-value=1 Score=27.99 Aligned_cols=32 Identities=16% Similarity=0.451 Sum_probs=19.6
Q ss_pred cceecccchhhcCCHHHHHHHHHhhCCCCcccccCccccC
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSR 91 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f~ 91 (101)
.-|.|+.|+..|+....+. --|.|+.||....
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME--------YGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHhh--------cCCcCCCCCCCCe
Confidence 3466777777766665542 2577777775443
No 62
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=80.15 E-value=1.2 Score=20.18 Aligned_cols=9 Identities=33% Similarity=0.855 Sum_probs=4.0
Q ss_pred eecccchhh
Q psy11364 54 ATCFVCGKQ 62 (101)
Q Consensus 54 ~~C~~c~~~ 62 (101)
..|..|+..
T Consensus 26 vrC~~C~~~ 34 (37)
T PF13719_consen 26 VRCPKCGHV 34 (37)
T ss_pred EECCCCCcE
Confidence 344444443
No 63
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=79.84 E-value=1.5 Score=19.81 Aligned_cols=10 Identities=50% Similarity=1.002 Sum_probs=4.4
Q ss_pred CcccccCccc
Q psy11364 80 FYACSSCSHV 89 (101)
Q Consensus 80 p~~C~~C~k~ 89 (101)
-..|..|+..
T Consensus 25 ~v~C~~C~~~ 34 (36)
T PF13717_consen 25 KVRCSKCGHV 34 (36)
T ss_pred EEECCCCCCE
Confidence 3444444443
No 64
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=79.47 E-value=0.46 Score=32.18 Aligned_cols=49 Identities=24% Similarity=0.455 Sum_probs=42.8
Q ss_pred cceecccchhhcCCHHHHHHHHH--hhCC---CCcccc--cCccccCChHHHhccc
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHME--THQN---AFYACS--SCSHVSRSRDALRKHD 100 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~--~h~~---kp~~C~--~C~k~f~~~~~l~~H~ 100 (101)
.++.|..|...+.....+..|.+ .|.+ +|+.|+ .|++.|.+...+..|.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 343 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHI 343 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCc
Confidence 36889999999999999999999 7876 499999 7999999999887774
No 65
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=79.07 E-value=1.4 Score=26.42 Aligned_cols=36 Identities=11% Similarity=0.351 Sum_probs=20.0
Q ss_pred cceecccchhhcCCHHHHHHHHHhhCCCCcccccCcccc
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVS 90 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f 90 (101)
..|.|+.|+..|.....+.. .....-|.|+.||...
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~---~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQL---LDMDGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCCEeeHHHHHHh---cCCCCcEECCCCCCEE
Confidence 34778888777765433221 0112237788887654
No 66
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=78.77 E-value=0.96 Score=22.91 Aligned_cols=32 Identities=25% Similarity=0.574 Sum_probs=19.0
Q ss_pred cceecccchhhcCCHH-HHHHHHHhhCCCCcccccCcc
Q psy11364 52 LFATCFVCGKQLSNQY-NLRVHMETHQNAFYACSSCSH 88 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~-~l~~h~~~h~~kp~~C~~C~k 88 (101)
-.|.|+.||+..-.+- ... -.+.+|.|+.||-
T Consensus 24 ~~F~CPnCG~~~I~RC~~CR-----k~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCEKCR-----KQSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeechhHH-----hcCCceECCCCCC
Confidence 3488999987622221 111 1126999999983
No 67
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=78.57 E-value=1.1 Score=27.60 Aligned_cols=23 Identities=30% Similarity=0.546 Sum_probs=13.6
Q ss_pred ceecccchhhcCCHHHHHHHHHhhCCCCcccccCc
Q psy11364 53 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCS 87 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~ 87 (101)
.|.|.+||..... . -|-.|++||
T Consensus 134 ~~vC~vCGy~~~g-e-----------~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTHEG-E-----------APEVCPICG 156 (166)
T ss_pred EEEcCCCCCcccC-C-----------CCCcCCCCC
Confidence 5777777643322 0 477777776
No 68
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=78.07 E-value=1.4 Score=20.94 Aligned_cols=8 Identities=25% Similarity=0.908 Sum_probs=3.9
Q ss_pred CcccccCc
Q psy11364 80 FYACSSCS 87 (101)
Q Consensus 80 p~~C~~C~ 87 (101)
+..|+.||
T Consensus 19 ~irC~~CG 26 (44)
T smart00659 19 VVRCRECG 26 (44)
T ss_pred ceECCCCC
Confidence 44455554
No 69
>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=77.71 E-value=1.5 Score=19.76 Aligned_cols=9 Identities=33% Similarity=0.803 Sum_probs=4.0
Q ss_pred eecccchhh
Q psy11364 54 ATCFVCGKQ 62 (101)
Q Consensus 54 ~~C~~c~~~ 62 (101)
..|+.|+..
T Consensus 26 v~C~~C~~~ 34 (38)
T TIGR02098 26 VRCGKCGHV 34 (38)
T ss_pred EECCCCCCE
Confidence 344444443
No 70
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=76.22 E-value=1.4 Score=25.96 Aligned_cols=15 Identities=20% Similarity=0.530 Sum_probs=7.8
Q ss_pred ceecccchhhcCCHH
Q psy11364 53 FATCFVCGKQLSNQY 67 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~ 67 (101)
|+.|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 345555555555433
No 71
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=76.01 E-value=1.6 Score=18.23 Aligned_cols=8 Identities=25% Similarity=0.721 Sum_probs=4.1
Q ss_pred cccCcccc
Q psy11364 83 CSSCSHVS 90 (101)
Q Consensus 83 C~~C~k~f 90 (101)
|++|++.+
T Consensus 4 CPiC~~~v 11 (26)
T smart00734 4 CPVCFREV 11 (26)
T ss_pred CCCCcCcc
Confidence 55555544
No 72
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=73.06 E-value=2.1 Score=32.12 Aligned_cols=60 Identities=20% Similarity=0.270 Sum_probs=39.5
Q ss_pred CCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhCCCCcccccCccccC
Q psy11364 26 SSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSR 91 (101)
Q Consensus 26 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f~ 91 (101)
.|..||-.|+--..+.-...... ...--.|+.|.+.|..+.+-+-| . .|..|+.||-...
T Consensus 125 ~CT~CGPRfTIi~alPYDR~nTs-M~~F~lC~~C~~EY~dP~nRRfH----A-Qp~aCp~CGP~~~ 184 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRENTS-MADFPLCPFCDKEYKDPLNRRFH----A-QPIACPKCGPHLF 184 (750)
T ss_pred ccCCCCcceeeeccCCCCcccCc-cccCcCCHHHHHHhcCccccccc----c-ccccCcccCCCeE
Confidence 57889988877666654433322 22223599999988887764433 3 6899999996443
No 73
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=72.65 E-value=1.5 Score=28.04 Aligned_cols=44 Identities=9% Similarity=0.068 Sum_probs=25.2
Q ss_pred CCCCCCCCCCCCccCCCCCCCCCC---------CCCCC-----cceecccchhhcCCH
Q psy11364 23 SPLSSSIPGSSKTKASGSGTTGGS---------SNHSK-----LFATCFVCGKQLSNQ 66 (101)
Q Consensus 23 ~~~~c~~c~~~~~~~~~~~~~~~~---------~~~~~-----~~~~C~~c~~~~~~~ 66 (101)
....||.|++.|..+.......+. .-.+. ....|+.||.++...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 356899999999776444332221 11111 235688888665543
No 74
>KOG2785|consensus
Probab=72.59 E-value=2.5 Score=29.37 Aligned_cols=22 Identities=23% Similarity=0.377 Sum_probs=17.7
Q ss_pred CCcccccCccccCChHHHhccc
Q psy11364 79 AFYACSSCSHVSRSRDALRKHD 100 (101)
Q Consensus 79 kp~~C~~C~k~f~~~~~l~~H~ 100 (101)
-++.|.+|.+.|........|+
T Consensus 67 ~~~~c~~c~k~~~s~~a~~~hl 88 (390)
T KOG2785|consen 67 SVVYCEACNKSFASPKAHENHL 88 (390)
T ss_pred cceehHHhhccccChhhHHHHH
Confidence 4788999999998887776664
No 75
>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=72.58 E-value=4.5 Score=24.16 Aligned_cols=20 Identities=30% Similarity=0.369 Sum_probs=11.5
Q ss_pred cceecccchhhcCCHHHHHH
Q psy11364 52 LFATCFVCGKQLSNQYNLRV 71 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~ 71 (101)
..+.|+.|++.|..-++..+
T Consensus 123 ~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 123 EFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred eEEECCCCCCEecccccHHH
Confidence 34566666666666555443
No 76
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=72.27 E-value=4.3 Score=30.80 Aligned_cols=47 Identities=17% Similarity=0.146 Sum_probs=26.8
Q ss_pred CCCCCCCCCCCccCCC---CCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhCCCCcccccCccc
Q psy11364 24 PLSSSIPGSSKTKASG---SGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 89 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~---~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~ 89 (101)
-..|..||..+..+.. +.-|. ..+...|..||..- ..|..|+.||..
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~-----~~~~L~CH~Cg~~~--------------~~p~~Cp~Cgs~ 484 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHK-----ATGQLRCHYCGYQE--------------PIPQSCPECGSE 484 (730)
T ss_pred eeecccCCCcccCCCCCcceEEec-----CCCeeEeCCCCCCC--------------CCCCCCCCCCCC
Confidence 4556777766544322 22232 23556788887431 158888888854
No 77
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=72.13 E-value=2.6 Score=22.28 Aligned_cols=41 Identities=7% Similarity=0.143 Sum_probs=23.9
Q ss_pred CCCCCCCCCCccCCCCCCCCCCCCCCCcceecc--cchhhcCCHHH
Q psy11364 25 LSSSIPGSSKTKASGSGTTGGSSNHSKLFATCF--VCGKQLSNQYN 68 (101)
Q Consensus 25 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~--~c~~~~~~~~~ 68 (101)
..|+.||......++-..... ..++.+.|. .||..|..-..
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~---~~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT---TKERYHQCQNVNCSATFITYES 44 (72)
T ss_pred ccCCCCCCccEEEEChhcChh---hheeeeecCCCCCCCEEEEEEE
Confidence 358888876533333222211 236667887 89888766543
No 78
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=71.77 E-value=1.5 Score=21.13 Aligned_cols=13 Identities=54% Similarity=1.002 Sum_probs=8.1
Q ss_pred eecccchhhcCCH
Q psy11364 54 ATCFVCGKQLSNQ 66 (101)
Q Consensus 54 ~~C~~c~~~~~~~ 66 (101)
-.|..|++.+...
T Consensus 19 a~C~~C~~~l~~~ 31 (50)
T smart00614 19 AKCKYCGKKLSRS 31 (50)
T ss_pred EEecCCCCEeeeC
Confidence 4577777766544
No 79
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=70.11 E-value=2.5 Score=23.92 Aligned_cols=12 Identities=25% Similarity=0.805 Sum_probs=6.5
Q ss_pred eecccchhhcCC
Q psy11364 54 ATCFVCGKQLSN 65 (101)
Q Consensus 54 ~~C~~c~~~~~~ 65 (101)
+.|..||..|..
T Consensus 3 H~CtrCG~vf~~ 14 (112)
T COG3364 3 HQCTRCGEVFDD 14 (112)
T ss_pred ceeccccccccc
Confidence 455555555554
No 80
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=69.88 E-value=0.94 Score=21.49 Aligned_cols=10 Identities=10% Similarity=0.026 Sum_probs=5.3
Q ss_pred CCCCCCCCCC
Q psy11364 25 LSSSIPGSSK 34 (101)
Q Consensus 25 ~~c~~c~~~~ 34 (101)
|.|+.||..+
T Consensus 4 y~C~~CG~~~ 13 (46)
T PRK00398 4 YKCARCGREV 13 (46)
T ss_pred EECCCCCCEE
Confidence 4555566543
No 81
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=69.31 E-value=3.3 Score=25.23 Aligned_cols=19 Identities=26% Similarity=0.382 Sum_probs=13.3
Q ss_pred CCcceecccchhhcCCHHH
Q psy11364 50 SKLFATCFVCGKQLSNQYN 68 (101)
Q Consensus 50 ~~~~~~C~~c~~~~~~~~~ 68 (101)
.+.|..|..||+.|.+-..
T Consensus 65 ~~~PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 65 YEAPSYCHNCGKPYPWTEN 83 (158)
T ss_pred CCCChhHHhCCCCCchHHH
Confidence 3567778888888776543
No 82
>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=69.30 E-value=5 Score=18.96 Aligned_cols=29 Identities=21% Similarity=0.227 Sum_probs=16.1
Q ss_pred CCCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchh
Q psy11364 23 SPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGK 61 (101)
Q Consensus 23 ~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~ 61 (101)
+.+.|+.||..- ...+ .....|.|..|++
T Consensus 17 ~g~~CP~Cg~~~--~~~~--------~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGSTK--HYRL--------KTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCee--eEEe--------CCCCeEECCCCCC
Confidence 467788888541 1111 1145578887764
No 83
>KOG1146|consensus
Probab=68.13 E-value=2.7 Score=33.76 Aligned_cols=72 Identities=18% Similarity=0.244 Sum_probs=51.3
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhC-----------------C-CCccccc
Q psy11364 24 PLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQ-----------------N-AFYACSS 85 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~-----------------~-kp~~C~~ 85 (101)
.+.|..|...+...-.+. +. ....+|.|..|...|.....|..|.+... . ++| |..
T Consensus 1260 e~~c~~~~~~~~~~~~~~-~l----~~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~ 1333 (1406)
T KOG1146|consen 1260 EGECGAVDELLTPSFGIS-TL----DVTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLA 1333 (1406)
T ss_pred cchhhhccccccCcccee-ec----ccchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chH
Confidence 455666665555544433 22 23567899999999999999998885332 2 567 999
Q ss_pred CccccCChHHHhcccC
Q psy11364 86 CSHVSRSRDALRKHDK 101 (101)
Q Consensus 86 C~k~f~~~~~l~~H~~ 101 (101)
|...|.....|+.|++
T Consensus 1334 c~~~~~~~~alqihm~ 1349 (1406)
T KOG1146|consen 1334 CEVLLSGREALQIHMR 1349 (1406)
T ss_pred HHhhcchhHHHHHHHH
Confidence 9999999999988874
No 84
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=68.07 E-value=4.1 Score=18.79 Aligned_cols=12 Identities=33% Similarity=0.935 Sum_probs=7.9
Q ss_pred cceecccchhhc
Q psy11364 52 LFATCFVCGKQL 63 (101)
Q Consensus 52 ~~~~C~~c~~~~ 63 (101)
.-|.|..|+..+
T Consensus 27 ~fy~C~~C~~~w 38 (40)
T smart00440 27 VFYVCTKCGHRW 38 (40)
T ss_pred EEEEeCCCCCEe
Confidence 347787777654
No 85
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=67.94 E-value=1.7 Score=24.01 Aligned_cols=12 Identities=33% Similarity=0.645 Sum_probs=5.8
Q ss_pred ceecccchhhcC
Q psy11364 53 FATCFVCGKQLS 64 (101)
Q Consensus 53 ~~~C~~c~~~~~ 64 (101)
|-.|..||..|.
T Consensus 58 Pa~CkkCGfef~ 69 (97)
T COG3357 58 PARCKKCGFEFR 69 (97)
T ss_pred ChhhcccCcccc
Confidence 344555554443
No 86
>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=67.87 E-value=4.4 Score=24.45 Aligned_cols=16 Identities=13% Similarity=0.449 Sum_probs=10.4
Q ss_pred eecccchhhcCCHHHH
Q psy11364 54 ATCFVCGKQLSNQYNL 69 (101)
Q Consensus 54 ~~C~~c~~~~~~~~~l 69 (101)
-.|..|++.|++-..+
T Consensus 29 ReC~~C~~RFTTyErv 44 (147)
T TIGR00244 29 RECLECHERFTTFERA 44 (147)
T ss_pred ccCCccCCccceeeec
Confidence 4677777777665543
No 87
>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=67.84 E-value=6.5 Score=18.15 Aligned_cols=23 Identities=39% Similarity=0.642 Sum_probs=13.2
Q ss_pred CcceecccchhhcCCH----HHHHHHH
Q psy11364 51 KLFATCFVCGKQLSNQ----YNLRVHM 73 (101)
Q Consensus 51 ~~~~~C~~c~~~~~~~----~~l~~h~ 73 (101)
.....|..|++.+... +.|.+|+
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 4456788888877664 5677776
No 88
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=66.86 E-value=1.9 Score=21.02 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=7.0
Q ss_pred ceecccchhhc
Q psy11364 53 FATCFVCGKQL 63 (101)
Q Consensus 53 ~~~C~~c~~~~ 63 (101)
.|.|..||+.+
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 36666676665
No 89
>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=66.39 E-value=2.7 Score=17.29 Aligned_cols=8 Identities=38% Similarity=0.733 Sum_probs=4.2
Q ss_pred ceecccch
Q psy11364 53 FATCFVCG 60 (101)
Q Consensus 53 ~~~C~~c~ 60 (101)
.|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 45555554
No 90
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=65.57 E-value=1.8 Score=23.74 Aligned_cols=10 Identities=30% Similarity=0.810 Sum_probs=5.5
Q ss_pred eecccchhhc
Q psy11364 54 ATCFVCGKQL 63 (101)
Q Consensus 54 ~~C~~c~~~~ 63 (101)
|.|..|+..|
T Consensus 54 W~C~kCg~~f 63 (89)
T COG1997 54 WKCRKCGAKF 63 (89)
T ss_pred EEcCCCCCee
Confidence 5565665544
No 91
>PF14353 CpXC: CpXC protein
Probab=65.46 E-value=2.6 Score=24.43 Aligned_cols=10 Identities=10% Similarity=-0.001 Sum_probs=6.6
Q ss_pred CCCCCCCCCc
Q psy11364 26 SSSIPGSSKT 35 (101)
Q Consensus 26 ~c~~c~~~~~ 35 (101)
.|+.||..|.
T Consensus 3 tCP~C~~~~~ 12 (128)
T PF14353_consen 3 TCPHCGHEFE 12 (128)
T ss_pred CCCCCCCeeE
Confidence 5777777653
No 92
>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=65.42 E-value=2.8 Score=26.89 Aligned_cols=21 Identities=24% Similarity=0.572 Sum_probs=15.0
Q ss_pred CcccccCccccCChHHHhccc
Q psy11364 80 FYACSSCSHVSRSRDALRKHD 100 (101)
Q Consensus 80 p~~C~~C~k~f~~~~~l~~H~ 100 (101)
-|.|.+|+|.|.-...+.+|+
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI 97 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHI 97 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHH
T ss_pred EECCCCCCcccCChHHHHHHH
Confidence 488888888888887777775
No 93
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=64.98 E-value=5.5 Score=24.18 Aligned_cols=16 Identities=19% Similarity=0.573 Sum_probs=10.5
Q ss_pred ceecccchhhcCCHHH
Q psy11364 53 FATCFVCGKQLSNQYN 68 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~ 68 (101)
.-.|..|+..|.+-..
T Consensus 28 RReC~~C~~RFTTfE~ 43 (156)
T COG1327 28 RRECLECGERFTTFER 43 (156)
T ss_pred hhcccccccccchhhe
Confidence 3467777777766554
No 94
>KOG4167|consensus
Probab=64.16 E-value=2.3 Score=32.16 Aligned_cols=26 Identities=31% Similarity=0.478 Sum_probs=23.4
Q ss_pred cceecccchhhcCCHHHHHHHHHhhC
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQ 77 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~ 77 (101)
--|.|..|+|.|.....+..||+.|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 34899999999999999999999886
No 95
>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=63.78 E-value=5 Score=16.74 Aligned_cols=13 Identities=15% Similarity=-0.136 Sum_probs=9.3
Q ss_pred CCCCCCCCCCCCc
Q psy11364 23 SPLSSSIPGSSKT 35 (101)
Q Consensus 23 ~~~~c~~c~~~~~ 35 (101)
..-.|+.||..|.
T Consensus 13 ~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 13 SAKFCPHCGYDFE 25 (26)
T ss_pred hcCcCCCCCCCCc
Confidence 3557888888774
No 96
>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=62.57 E-value=5.9 Score=23.47 Aligned_cols=25 Identities=32% Similarity=0.801 Sum_probs=16.3
Q ss_pred CcceecccchhhcCCHHHHHHHHHhhCC
Q psy11364 51 KLFATCFVCGKQLSNQYNLRVHMETHQN 78 (101)
Q Consensus 51 ~~~~~C~~c~~~~~~~~~l~~h~~~h~~ 78 (101)
+....|-.||+.|.. |++|++.|.|
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-
T ss_pred cCeeEEccCCcccch---HHHHHHHccC
Confidence 455789999999987 5899998854
No 97
>PLN02294 cytochrome c oxidase subunit Vb
Probab=62.39 E-value=3.6 Score=25.45 Aligned_cols=22 Identities=14% Similarity=0.339 Sum_probs=16.3
Q ss_pred HHHHhhCCCCcccccCccccCC
Q psy11364 71 VHMETHQNAFYACSSCSHVSRS 92 (101)
Q Consensus 71 ~h~~~h~~kp~~C~~C~k~f~~ 92 (101)
.++.++.++|++|++||..|.-
T Consensus 132 ~Wf~L~kGkp~RCpeCG~~fkL 153 (174)
T PLN02294 132 VWFWLEKGKSFECPVCTQYFEL 153 (174)
T ss_pred EEEEecCCCceeCCCCCCEEEE
Confidence 3444555699999999988753
No 98
>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=62.03 E-value=3 Score=18.38 Aligned_cols=9 Identities=33% Similarity=0.922 Sum_probs=3.9
Q ss_pred CcccccCcc
Q psy11364 80 FYACSSCSH 88 (101)
Q Consensus 80 p~~C~~C~k 88 (101)
+..|..||.
T Consensus 17 ~irC~~CG~ 25 (32)
T PF03604_consen 17 PIRCPECGH 25 (32)
T ss_dssp TSSBSSSS-
T ss_pred cEECCcCCC
Confidence 344555543
No 99
>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=61.93 E-value=3.3 Score=18.70 Aligned_cols=11 Identities=36% Similarity=1.056 Sum_probs=7.8
Q ss_pred cccccCccccC
Q psy11364 81 YACSSCSHVSR 91 (101)
Q Consensus 81 ~~C~~C~k~f~ 91 (101)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 67777877664
No 100
>PF15269 zf-C2H2_7: Zinc-finger
Probab=61.03 E-value=3.9 Score=19.57 Aligned_cols=20 Identities=30% Similarity=0.526 Sum_probs=11.9
Q ss_pred eecccchhhcCCHHHHHHHH
Q psy11364 54 ATCFVCGKQLSNQYNLRVHM 73 (101)
Q Consensus 54 ~~C~~c~~~~~~~~~l~~h~ 73 (101)
|.|-.|.-....++.|-.||
T Consensus 21 ykcfqcpftc~~kshl~nhm 40 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHM 40 (54)
T ss_pred ceeecCCcccchHHHHHHHH
Confidence 45666665555566666555
No 101
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=60.19 E-value=3.9 Score=22.89 Aligned_cols=20 Identities=25% Similarity=0.445 Sum_probs=15.0
Q ss_pred HHHhhCCCCcccccCccccC
Q psy11364 72 HMETHQNAFYACSSCSHVSR 91 (101)
Q Consensus 72 h~~~h~~kp~~C~~C~k~f~ 91 (101)
++.++.++|++|..||..|.
T Consensus 71 W~~l~~g~~~rC~eCG~~fk 90 (97)
T cd00924 71 WMWLEKGKPKRCPECGHVFK 90 (97)
T ss_pred EEEEeCCCceeCCCCCcEEE
Confidence 34445568999999998875
No 102
>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=59.45 E-value=9.5 Score=24.52 Aligned_cols=25 Identities=24% Similarity=0.344 Sum_probs=20.4
Q ss_pred CcceecccchhhcCCHHHHHHHHHh
Q psy11364 51 KLFATCFVCGKQLSNQYNLRVHMET 75 (101)
Q Consensus 51 ~~~~~C~~c~~~~~~~~~l~~h~~~ 75 (101)
+..|.|..|+|.|....-+..|+..
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhh
Confidence 5569999999999999999999875
No 103
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=58.62 E-value=3.9 Score=19.00 Aligned_cols=11 Identities=36% Similarity=0.990 Sum_probs=7.4
Q ss_pred cccccCccccC
Q psy11364 81 YACSSCSHVSR 91 (101)
Q Consensus 81 ~~C~~C~k~f~ 91 (101)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 66777776664
No 104
>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=58.59 E-value=2.4 Score=19.47 Aligned_cols=12 Identities=42% Similarity=1.021 Sum_probs=8.1
Q ss_pred cceecccchhhc
Q psy11364 52 LFATCFVCGKQL 63 (101)
Q Consensus 52 ~~~~C~~c~~~~ 63 (101)
.-|.|..|+..|
T Consensus 27 ~fy~C~~C~~~w 38 (39)
T PF01096_consen 27 LFYVCCNCGHRW 38 (39)
T ss_dssp EEEEESSSTEEE
T ss_pred EEEEeCCCCCee
Confidence 347788887654
No 105
>KOG2785|consensus
Probab=57.37 E-value=13 Score=26.06 Aligned_cols=50 Identities=22% Similarity=0.378 Sum_probs=39.8
Q ss_pred cceecccchhhcCCHHHHHHHHHhhC------------------------CCCcccccCc---cccCChHHHhcccC
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQ------------------------NAFYACSSCS---HVSRSRDALRKHDK 101 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~------------------------~kp~~C~~C~---k~f~~~~~l~~H~~ 101 (101)
.|-.|-.|++.+..-..-..||-.+. +.-+.|..|. +.|......+.||.
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 45678889998888888888887654 2467898998 89999999998873
No 106
>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=56.73 E-value=19 Score=17.51 Aligned_cols=13 Identities=23% Similarity=0.094 Sum_probs=8.6
Q ss_pred CCCCCCCCCCccC
Q psy11364 25 LSSSIPGSSKTKA 37 (101)
Q Consensus 25 ~~c~~c~~~~~~~ 37 (101)
|.|..||..+...
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 5677777766544
No 107
>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=56.67 E-value=11 Score=27.19 Aligned_cols=10 Identities=30% Similarity=0.574 Sum_probs=5.8
Q ss_pred cceecccchh
Q psy11364 52 LFATCFVCGK 61 (101)
Q Consensus 52 ~~~~C~~c~~ 61 (101)
+...|..||.
T Consensus 239 ~~l~Ch~Cg~ 248 (505)
T TIGR00595 239 GKLRCHYCGY 248 (505)
T ss_pred CeEEcCCCcC
Confidence 3456666663
No 108
>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=55.98 E-value=21 Score=20.12 Aligned_cols=38 Identities=8% Similarity=0.037 Sum_probs=25.9
Q ss_pred cceecccchhhcCCHHHHHHHHHhhCCCCcccccCccc
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 89 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~ 89 (101)
..|.|+.-+..|..-......+.....+-+.|...|+.
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~y~~~vwtC~~TGk~ 39 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMILYNQRVWTCEITGKS 39 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHHHhCCeeEEecCCCC
Confidence 34667777777777777766666555567777777764
No 109
>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=55.46 E-value=3.3 Score=17.70 Aligned_cols=8 Identities=38% Similarity=0.783 Sum_probs=3.7
Q ss_pred cccCcccc
Q psy11364 83 CSSCSHVS 90 (101)
Q Consensus 83 C~~C~k~f 90 (101)
|..|++.|
T Consensus 3 CiDC~~~F 10 (28)
T PF08790_consen 3 CIDCSKDF 10 (28)
T ss_dssp ETTTTEEE
T ss_pred eecCCCCc
Confidence 44444444
No 110
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=52.25 E-value=7.1 Score=17.89 Aligned_cols=14 Identities=14% Similarity=0.508 Sum_probs=10.0
Q ss_pred CcccccCccccCCh
Q psy11364 80 FYACSSCSHVSRSR 93 (101)
Q Consensus 80 p~~C~~C~k~f~~~ 93 (101)
|+.|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 77788887777543
No 111
>KOG2593|consensus
Probab=52.11 E-value=9.9 Score=27.01 Aligned_cols=18 Identities=39% Similarity=0.658 Sum_probs=11.3
Q ss_pred CCcccccCccccCChHHH
Q psy11364 79 AFYACSSCSHVSRSRDAL 96 (101)
Q Consensus 79 kp~~C~~C~k~f~~~~~l 96 (101)
..|.|+.|.+.|.....+
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~ 144 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEAL 144 (436)
T ss_pred ccccCCccccchhhhHHH
Confidence 567777777766655443
No 112
>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=51.63 E-value=6.1 Score=18.98 Aligned_cols=11 Identities=36% Similarity=1.053 Sum_probs=7.2
Q ss_pred cccccCccccC
Q psy11364 81 YACSSCSHVSR 91 (101)
Q Consensus 81 ~~C~~C~k~f~ 91 (101)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 56777776554
No 113
>PRK04023 DNA polymerase II large subunit; Validated
Probab=51.42 E-value=21 Score=28.43 Aligned_cols=11 Identities=9% Similarity=-0.000 Sum_probs=6.9
Q ss_pred CCCCCCCCCCC
Q psy11364 23 SPLSSSIPGSS 33 (101)
Q Consensus 23 ~~~~c~~c~~~ 33 (101)
....|+.||..
T Consensus 625 g~RfCpsCG~~ 635 (1121)
T PRK04023 625 GRRKCPSCGKE 635 (1121)
T ss_pred cCccCCCCCCc
Confidence 35667777764
No 114
>KOG4173|consensus
Probab=51.38 E-value=6.3 Score=25.28 Aligned_cols=46 Identities=20% Similarity=0.512 Sum_probs=26.2
Q ss_pred ecccchhhcCCHHHHHHHHH-hhC---------C-CCccc--ccCccccCChHHHhccc
Q psy11364 55 TCFVCGKQLSNQYNLRVHME-THQ---------N-AFYAC--SSCSHVSRSRDALRKHD 100 (101)
Q Consensus 55 ~C~~c~~~~~~~~~l~~h~~-~h~---------~-kp~~C--~~C~k~f~~~~~l~~H~ 100 (101)
.|..|.++|.+..-|..|+- +|. | --|.| +.|+-.|.+......|+
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~ 166 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHM 166 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHH
Confidence 56667777766666666643 232 3 34666 33666666655555443
No 115
>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=51.29 E-value=18 Score=18.31 Aligned_cols=34 Identities=24% Similarity=0.343 Sum_probs=20.2
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHH
Q psy11364 24 PLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYN 68 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~ 68 (101)
+-.|+.||..-.. ....+.|.|+.||......-+
T Consensus 28 Sq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~~~~rD~n 61 (69)
T PF07282_consen 28 SQTCPRCGHRNKK-----------RRSGRVFTCPNCGFEMDRDVN 61 (69)
T ss_pred ccCccCccccccc-----------ccccceEEcCCCCCEECcHHH
Confidence 4557777753322 123566888888877655443
No 116
>PHA02998 RNA polymerase subunit; Provisional
Probab=50.97 E-value=9.9 Score=23.80 Aligned_cols=14 Identities=21% Similarity=0.425 Sum_probs=8.7
Q ss_pred ceecccchhhcCCH
Q psy11364 53 FATCFVCGKQLSNQ 66 (101)
Q Consensus 53 ~~~C~~c~~~~~~~ 66 (101)
.|.|..|++.|..+
T Consensus 171 FYkC~~CG~~wkpp 184 (195)
T PHA02998 171 RHACRDCKKHFKPP 184 (195)
T ss_pred EEEcCCCCCccCCc
Confidence 36677777666543
No 117
>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=50.91 E-value=7.1 Score=16.91 Aligned_cols=9 Identities=33% Similarity=0.936 Sum_probs=4.7
Q ss_pred ceecccchh
Q psy11364 53 FATCFVCGK 61 (101)
Q Consensus 53 ~~~C~~c~~ 61 (101)
.+.|+.|+.
T Consensus 19 ~~vCp~C~~ 27 (30)
T PF08274_consen 19 LLVCPECGH 27 (30)
T ss_dssp SEEETTTTE
T ss_pred EEeCCcccc
Confidence 355555543
No 118
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=49.48 E-value=5 Score=18.68 Aligned_cols=15 Identities=13% Similarity=0.406 Sum_probs=8.0
Q ss_pred CCcccccCccccCCh
Q psy11364 79 AFYACSSCSHVSRSR 93 (101)
Q Consensus 79 kp~~C~~C~k~f~~~ 93 (101)
.|+.|..|++.|-..
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 367777777777543
No 119
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=49.30 E-value=15 Score=17.88 Aligned_cols=10 Identities=30% Similarity=0.451 Sum_probs=6.1
Q ss_pred ceecccchhh
Q psy11364 53 FATCFVCGKQ 62 (101)
Q Consensus 53 ~~~C~~c~~~ 62 (101)
.+.|..|+..
T Consensus 37 r~~C~~Cgyt 46 (50)
T PRK00432 37 RWHCGKCGYT 46 (50)
T ss_pred cEECCCcCCE
Confidence 4667777643
No 120
>PRK14873 primosome assembly protein PriA; Provisional
Probab=49.14 E-value=14 Score=27.84 Aligned_cols=46 Identities=15% Similarity=0.277 Sum_probs=25.0
Q ss_pred CCCCCCCCCCCccCCC---CCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhCCCCcccccCccc
Q psy11364 24 PLSSSIPGSSKTKASG---SGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 89 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~---~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~ 89 (101)
-..|..||........ +..|. ..+...|..||... .|..|+.||..
T Consensus 383 ~l~C~~Cg~~~~C~~C~~~L~~h~-----~~~~l~Ch~CG~~~---------------~p~~Cp~Cgs~ 431 (665)
T PRK14873 383 SLACARCRTPARCRHCTGPLGLPS-----AGGTPRCRWCGRAA---------------PDWRCPRCGSD 431 (665)
T ss_pred eeEhhhCcCeeECCCCCCceeEec-----CCCeeECCCCcCCC---------------cCccCCCCcCC
Confidence 3466666665544322 22221 23456788887421 26678888754
No 121
>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=48.80 E-value=9.6 Score=21.76 Aligned_cols=26 Identities=23% Similarity=0.571 Sum_probs=16.7
Q ss_pred ceecccchhhcCCHHHHHHHHHhhCCCCcccccCccc
Q psy11364 53 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 89 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~ 89 (101)
...|..|+..|..... .+.|+.||..
T Consensus 70 ~~~C~~Cg~~~~~~~~-----------~~~CP~Cgs~ 95 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEF-----------DFSCPRCGSP 95 (113)
T ss_dssp EEEETTTS-EEECHHC-----------CHH-SSSSSS
T ss_pred cEECCCCCCEEecCCC-----------CCCCcCCcCC
Confidence 3679999988866442 3568888864
No 122
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.33 E-value=5.8 Score=23.48 Aligned_cols=14 Identities=29% Similarity=0.548 Sum_probs=8.8
Q ss_pred cceecccchhhcCC
Q psy11364 52 LFATCFVCGKQLSN 65 (101)
Q Consensus 52 ~~~~C~~c~~~~~~ 65 (101)
..+.|..||..|..
T Consensus 69 ~~~~C~~CG~~~~~ 82 (135)
T PRK03824 69 AVLKCRNCGNEWSL 82 (135)
T ss_pred eEEECCCCCCEEec
Confidence 34677777766654
No 123
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=47.05 E-value=22 Score=24.16 Aligned_cols=10 Identities=20% Similarity=0.052 Sum_probs=7.5
Q ss_pred CCCCCCCCCC
Q psy11364 24 PLSSSIPGSS 33 (101)
Q Consensus 24 ~~~c~~c~~~ 33 (101)
.-.|+.||..
T Consensus 184 ~~~CPvCGs~ 193 (305)
T TIGR01562 184 RTLCPACGSP 193 (305)
T ss_pred CCcCCCCCCh
Confidence 4579999963
No 124
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.06 E-value=19 Score=21.31 Aligned_cols=17 Identities=18% Similarity=0.374 Sum_probs=11.9
Q ss_pred CcceecccchhhcCCHH
Q psy11364 51 KLFATCFVCGKQLSNQY 67 (101)
Q Consensus 51 ~~~~~C~~c~~~~~~~~ 67 (101)
+-|-.|.-||+.|..-.
T Consensus 66 e~psfchncgs~fpwte 82 (160)
T COG4306 66 EPPSFCHNCGSRFPWTE 82 (160)
T ss_pred CCcchhhcCCCCCCcHH
Confidence 45567888888876644
No 125
>KOG2907|consensus
Probab=45.21 E-value=8.2 Score=22.23 Aligned_cols=37 Identities=19% Similarity=0.556 Sum_probs=22.7
Q ss_pred eecccchhhcCCHHHHHHHHHh-hCC--CCcccccCccccCC
Q psy11364 54 ATCFVCGKQLSNQYNLRVHMET-HQN--AFYACSSCSHVSRS 92 (101)
Q Consensus 54 ~~C~~c~~~~~~~~~l~~h~~~-h~~--kp~~C~~C~k~f~~ 92 (101)
..|+.||..-..-.. ..+|. ..| .-|.|+.|+..|..
T Consensus 75 ~kCpkCghe~m~Y~T--~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHT--LQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhh--hhcccccCCceEEEEcCccceeeec
Confidence 679999843222222 22333 334 68999999988864
No 126
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=44.63 E-value=13 Score=21.30 Aligned_cols=13 Identities=38% Similarity=0.914 Sum_probs=9.1
Q ss_pred CCcccccCccccC
Q psy11364 79 AFYACSSCSHVSR 91 (101)
Q Consensus 79 kp~~C~~C~k~f~ 91 (101)
.-|.|..||..|+
T Consensus 99 ~Fy~C~~Cg~~wr 111 (113)
T COG1594 99 RFYKCTRCGYRWR 111 (113)
T ss_pred EEEEecccCCEee
Confidence 5677877876654
No 127
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.52 E-value=15 Score=21.17 Aligned_cols=13 Identities=15% Similarity=-0.028 Sum_probs=8.2
Q ss_pred Ccceecccchhhc
Q psy11364 51 KLFATCFVCGKQL 63 (101)
Q Consensus 51 ~~~~~C~~c~~~~ 63 (101)
+.|..|+.||+.|
T Consensus 24 rdPiVsPytG~s~ 36 (129)
T COG4530 24 RDPIVSPYTGKSY 36 (129)
T ss_pred CCccccCcccccc
Confidence 4556666666666
No 128
>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=43.46 E-value=13 Score=17.43 Aligned_cols=12 Identities=25% Similarity=0.534 Sum_probs=6.0
Q ss_pred ccccCccccCCh
Q psy11364 82 ACSSCSHVSRSR 93 (101)
Q Consensus 82 ~C~~C~k~f~~~ 93 (101)
.|.+||+.|++.
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 355555555543
No 129
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=43.40 E-value=4.3 Score=22.42 Aligned_cols=10 Identities=30% Similarity=0.551 Sum_probs=6.2
Q ss_pred eecccchhhc
Q psy11364 54 ATCFVCGKQL 63 (101)
Q Consensus 54 ~~C~~c~~~~ 63 (101)
|.|..|++.|
T Consensus 55 W~C~~C~~~~ 64 (90)
T PTZ00255 55 WRCKGCKKTV 64 (90)
T ss_pred EEcCCCCCEE
Confidence 6666666544
No 130
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=43.38 E-value=6.8 Score=19.65 Aligned_cols=7 Identities=29% Similarity=0.605 Sum_probs=3.5
Q ss_pred eecccch
Q psy11364 54 ATCFVCG 60 (101)
Q Consensus 54 ~~C~~c~ 60 (101)
|-|..|.
T Consensus 32 YmC~eC~ 38 (56)
T PF09963_consen 32 YMCDECK 38 (56)
T ss_pred eeChhHH
Confidence 5555553
No 131
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=42.51 E-value=8.9 Score=18.68 Aligned_cols=15 Identities=13% Similarity=0.257 Sum_probs=8.6
Q ss_pred CCcccccCccccCCh
Q psy11364 79 AFYACSSCSHVSRSR 93 (101)
Q Consensus 79 kp~~C~~C~k~f~~~ 93 (101)
+.+.|..||..|...
T Consensus 3 k~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFT 17 (49)
T ss_pred eeEEcccCCCeEEEe
Confidence 345666666665543
No 132
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=42.35 E-value=34 Score=22.76 Aligned_cols=51 Identities=16% Similarity=0.083 Sum_probs=31.4
Q ss_pred cccccceeeeeeeccccC--CCCCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhh
Q psy11364 4 NYKRSTLHFLISVSDHCL--TSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQ 62 (101)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~--~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~ 62 (101)
.+..+++.|+..+..... ...-.||.||..+.-..++ ..---|+|..|.-+
T Consensus 198 ~T~iPtYYyLyrv~g~~~~~e~~r~CP~Cg~~W~L~~pl--------h~iFdFKCD~CRLV 250 (258)
T PF10071_consen 198 LTGIPTYYYLYRVGGESLASEQARKCPSCGGDWRLKEPL--------HDIFDFKCDPCRLV 250 (258)
T ss_pred HhCCCeEEEEEEccCcchHHhhCCCCCCCCCccccCCch--------hhceeccCCcceee
Confidence 356677777777654432 2477888888877555443 12344778877543
No 133
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=41.49 E-value=34 Score=15.74 Aligned_cols=24 Identities=29% Similarity=0.567 Sum_probs=15.8
Q ss_pred eecccchhhcC--CHHHHHHHHHhhC
Q psy11364 54 ATCFVCGKQLS--NQYNLRVHMETHQ 77 (101)
Q Consensus 54 ~~C~~c~~~~~--~~~~l~~h~~~h~ 77 (101)
-.|..||..|. .+.....|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 47999997654 4455666766554
No 134
>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=41.46 E-value=36 Score=19.27 Aligned_cols=37 Identities=19% Similarity=0.367 Sum_probs=17.3
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccch
Q psy11364 24 PLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCG 60 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~ 60 (101)
|-.|+-||..-...+...........+.-.|.|..|+
T Consensus 2 p~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~ 38 (102)
T PF11672_consen 2 PIICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCD 38 (102)
T ss_pred CcccCCCCCeeEEcccchhcCccCCCCceeEECCCCC
Confidence 4567778764333222222222222223337787775
No 135
>PRK12496 hypothetical protein; Provisional
Probab=41.24 E-value=15 Score=22.44 Aligned_cols=29 Identities=21% Similarity=0.464 Sum_probs=18.6
Q ss_pred cceecccchhhcCCHHHHHHHHHhhCCCCcccccCccccC
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSR 91 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f~ 91 (101)
..+.|..|++.|.... ..-.|+.||....
T Consensus 126 w~~~C~gC~~~~~~~~-----------~~~~C~~CG~~~~ 154 (164)
T PRK12496 126 WRKVCKGCKKKYPEDY-----------PDDVCEICGSPVK 154 (164)
T ss_pred eeEECCCCCccccCCC-----------CCCcCCCCCChhh
Confidence 3478999998875321 1135899986543
No 136
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=41.24 E-value=12 Score=22.74 Aligned_cols=34 Identities=18% Similarity=0.420 Sum_probs=19.8
Q ss_pred cceecccchhhcCCHHHHHHHHHhhCCCCcccccCccc
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 89 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~ 89 (101)
-+|.|. |+..+.... +|-.+-.|+-|.|..|+..
T Consensus 116 ~~Y~C~-C~q~~l~~R---Rhn~~~~g~~YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLRIR---RHNTVRRGEVYRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccchhh---hcccccccceEEeccCCce
Confidence 357887 887754432 3322222346888888754
No 137
>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=41.06 E-value=31 Score=19.33 Aligned_cols=24 Identities=21% Similarity=0.412 Sum_probs=19.9
Q ss_pred eec----ccchhhcCCHHHHHHHHHhhC
Q psy11364 54 ATC----FVCGKQLSNQYNLRVHMETHQ 77 (101)
Q Consensus 54 ~~C----~~c~~~~~~~~~l~~h~~~h~ 77 (101)
|.| ..|+........+..|.+.+.
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 788 889999999999999887643
No 138
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=41.02 E-value=13 Score=24.24 Aligned_cols=18 Identities=17% Similarity=0.573 Sum_probs=13.9
Q ss_pred hhCCCCcccccCccccCC
Q psy11364 75 THQNAFYACSSCSHVSRS 92 (101)
Q Consensus 75 ~h~~kp~~C~~C~k~f~~ 92 (101)
++.+++.+|..||..|.-
T Consensus 176 LrEGkpqRCpECGqVFKL 193 (268)
T PTZ00043 176 CREGFLYRCGECDQIFML 193 (268)
T ss_pred ecCCCCccCCCCCcEEEE
Confidence 344589999999988753
No 139
>KOG2071|consensus
Probab=40.86 E-value=19 Score=26.64 Aligned_cols=27 Identities=22% Similarity=0.461 Sum_probs=23.0
Q ss_pred CcceecccchhhcCCHHHHHHHHHhhC
Q psy11364 51 KLFATCFVCGKQLSNQYNLRVHMETHQ 77 (101)
Q Consensus 51 ~~~~~C~~c~~~~~~~~~l~~h~~~h~ 77 (101)
..+..|..||..|........||..|.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 456889999999999998888888776
No 140
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=40.40 E-value=36 Score=16.02 Aligned_cols=12 Identities=25% Similarity=0.456 Sum_probs=8.0
Q ss_pred ceecccchhhcC
Q psy11364 53 FATCFVCGKQLS 64 (101)
Q Consensus 53 ~~~C~~c~~~~~ 64 (101)
.+.|+.|+..+.
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 577888885443
No 141
>PRK05580 primosome assembly protein PriA; Validated
Probab=40.38 E-value=29 Score=26.19 Aligned_cols=8 Identities=38% Similarity=0.953 Sum_probs=4.1
Q ss_pred ceecccch
Q psy11364 53 FATCFVCG 60 (101)
Q Consensus 53 ~~~C~~c~ 60 (101)
...|..||
T Consensus 408 ~l~Ch~Cg 415 (679)
T PRK05580 408 RLRCHHCG 415 (679)
T ss_pred eEECCCCc
Confidence 34555555
No 142
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=40.12 E-value=14 Score=21.16 Aligned_cols=25 Identities=20% Similarity=0.441 Sum_probs=15.2
Q ss_pred ceecccchhhcCCHHHHHHHHHhhCCCCcccccCcc
Q psy11364 53 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSH 88 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k 88 (101)
...|..|+..|.... ..+.|+.||.
T Consensus 70 ~~~C~~Cg~~~~~~~-----------~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ-----------HDAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCC-----------cCccCcCCCC
Confidence 367888886654422 2345888874
No 143
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=39.36 E-value=30 Score=21.40 Aligned_cols=20 Identities=30% Similarity=0.442 Sum_probs=10.9
Q ss_pred ceecccchhhcCCHHHHHHH
Q psy11364 53 FATCFVCGKQLSNQYNLRVH 72 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h 72 (101)
.+.|+.||+.|...++...-
T Consensus 130 f~~C~~CgkiYW~GsHw~~m 149 (165)
T COG1656 130 FYRCPKCGKIYWKGSHWRRM 149 (165)
T ss_pred eeECCCCcccccCchHHHHH
Confidence 34566666666555555433
No 144
>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=39.24 E-value=11 Score=18.36 Aligned_cols=12 Identities=17% Similarity=0.534 Sum_probs=6.2
Q ss_pred ccccCccccCCh
Q psy11364 82 ACSSCSHVSRSR 93 (101)
Q Consensus 82 ~C~~C~k~f~~~ 93 (101)
.|++|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 899999888643
No 145
>KOG3408|consensus
Probab=39.24 E-value=12 Score=21.94 Aligned_cols=23 Identities=17% Similarity=0.369 Sum_probs=16.1
Q ss_pred CcceecccchhhcCCHHHHHHHH
Q psy11364 51 KLFATCFVCGKQLSNQYNLRVHM 73 (101)
Q Consensus 51 ~~~~~C~~c~~~~~~~~~l~~h~ 73 (101)
.-.|.|-.|.+-|.....+..|.
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~ 77 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHF 77 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHH
Confidence 34577778888887777776653
No 146
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.08 E-value=52 Score=19.00 Aligned_cols=12 Identities=33% Similarity=0.764 Sum_probs=6.0
Q ss_pred CcccccCccccC
Q psy11364 80 FYACSSCSHVSR 91 (101)
Q Consensus 80 p~~C~~C~k~f~ 91 (101)
.|.|+.|...|-
T Consensus 81 ~y~C~~C~~~FC 92 (112)
T TIGR00622 81 RYVCAVCKNVFC 92 (112)
T ss_pred ceeCCCCCCccc
Confidence 455555554443
No 147
>PLN02748 tRNA dimethylallyltransferase
Probab=39.04 E-value=18 Score=26.14 Aligned_cols=22 Identities=27% Similarity=0.693 Sum_probs=11.0
Q ss_pred CCcccccCcc-ccCChHHHhccc
Q psy11364 79 AFYACSSCSH-VSRSRDALRKHD 100 (101)
Q Consensus 79 kp~~C~~C~k-~f~~~~~l~~H~ 100 (101)
+.|.|+.|++ .+........|+
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hl 439 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHK 439 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHh
Confidence 3455555554 455444444443
No 148
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=37.91 E-value=16 Score=21.04 Aligned_cols=26 Identities=19% Similarity=0.416 Sum_probs=15.4
Q ss_pred ceecccchhhcCCHHHHHHHHHhhCCCCc-ccccCccc
Q psy11364 53 FATCFVCGKQLSNQYNLRVHMETHQNAFY-ACSSCSHV 89 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h~~~h~~kp~-~C~~C~k~ 89 (101)
...|..|+..|..... .+ .|+.||..
T Consensus 71 ~~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs~ 97 (117)
T PRK00564 71 ELECKDCSHVFKPNAL-----------DYGVCEKCHSK 97 (117)
T ss_pred EEEhhhCCCccccCCc-----------cCCcCcCCCCC
Confidence 3678888866544321 23 48888753
No 149
>KOG2636|consensus
Probab=37.77 E-value=22 Score=25.58 Aligned_cols=25 Identities=32% Similarity=0.610 Sum_probs=14.7
Q ss_pred hhCC-CCcccccCc-cccCChHHHhcc
Q psy11364 75 THQN-AFYACSSCS-HVSRSRDALRKH 99 (101)
Q Consensus 75 ~h~~-kp~~C~~C~-k~f~~~~~l~~H 99 (101)
.|.- ..|.|.+|| +++.-.....+|
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRH 421 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHH
Confidence 3444 678888887 555555444444
No 150
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=37.49 E-value=17 Score=17.72 Aligned_cols=39 Identities=18% Similarity=0.335 Sum_probs=20.0
Q ss_pred cceeccc--chhhcCCHHHHHHHHHhhCC-CCccccc----CccccC
Q psy11364 52 LFATCFV--CGKQLSNQYNLRVHMETHQN-AFYACSS----CSHVSR 91 (101)
Q Consensus 52 ~~~~C~~--c~~~~~~~~~l~~h~~~h~~-kp~~C~~----C~k~f~ 91 (101)
.+..|+. |...+. +..|..|....=. ++..|.. |+..+.
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred CEeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 4456765 434343 4457888874333 6677777 766654
No 151
>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=37.04 E-value=9.9 Score=22.68 Aligned_cols=18 Identities=22% Similarity=0.451 Sum_probs=13.8
Q ss_pred HhhCCCCcccccCccccC
Q psy11364 74 ETHQNAFYACSSCSHVSR 91 (101)
Q Consensus 74 ~~h~~kp~~C~~C~k~f~ 91 (101)
.++.++|.+|..||..|.
T Consensus 106 ~l~~g~~~RCpeCG~~fk 123 (136)
T PF01215_consen 106 WLHKGKPQRCPECGQVFK 123 (136)
T ss_dssp EEETTSEEEETTTEEEEE
T ss_pred EEeCCCccCCCCCCeEEE
Confidence 344458999999998875
No 152
>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=36.95 E-value=7.1 Score=23.21 Aligned_cols=33 Identities=21% Similarity=0.558 Sum_probs=20.9
Q ss_pred cceecccchhhcCCHHHHHHHHHhhCCCCcccccCccccC
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSR 91 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f~ 91 (101)
-.|.|..|+..+.. +.++ ..+-|.|..|+..+.
T Consensus 122 ~~~~C~~C~~~~~r------~~~~-~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 122 YVYRCPSCGREYKR------HRRS-KRKRYRCGRCGGPLV 154 (157)
T ss_pred eEEEcCCCCCEeee------eccc-chhhEECCCCCCEEE
Confidence 34789999866532 2233 114588999987654
No 153
>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=36.31 E-value=4.9 Score=22.24 Aligned_cols=10 Identities=40% Similarity=0.889 Sum_probs=5.9
Q ss_pred eecccchhhc
Q psy11364 54 ATCFVCGKQL 63 (101)
Q Consensus 54 ~~C~~c~~~~ 63 (101)
|.|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (91)
T TIGR00280 54 WTCRKCGAKF 63 (91)
T ss_pred EEcCCCCCEE
Confidence 5666666544
No 154
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=36.09 E-value=16 Score=27.83 Aligned_cols=59 Identities=19% Similarity=0.243 Sum_probs=36.2
Q ss_pred CCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHHHHHHhhCCCCcccccCcccc
Q psy11364 26 SSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVS 90 (101)
Q Consensus 26 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f 90 (101)
.|..||-.|.-..++.-...... ....-.|+.|.+.+..+.+- +-|. .+-.|..||-..
T Consensus 92 nCt~CGPr~~i~~~lpydr~~t~-m~~f~~C~~C~~ey~~p~~r----r~h~-~~~~C~~Cgp~l 150 (711)
T TIGR00143 92 SCTHCGPRFTIIEALPYDRENTS-MADFPLCPDCAKEYKDPLDR----RFHA-QPIACPRCGPQL 150 (711)
T ss_pred cccCCCCCeEEeecCCCCCCCcC-CCCCcCCHHHHHHhcCCccc----cCCC-CCccCCCCCcEE
Confidence 57889988866666543332222 23333599998887766432 2222 577899998654
No 155
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=36.08 E-value=42 Score=22.91 Aligned_cols=11 Identities=18% Similarity=0.087 Sum_probs=8.4
Q ss_pred CCCCCCCCCCC
Q psy11364 23 SPLSSSIPGSS 33 (101)
Q Consensus 23 ~~~~c~~c~~~ 33 (101)
....|+.||..
T Consensus 186 ~~~~CPvCGs~ 196 (309)
T PRK03564 186 QRQFCPVCGSM 196 (309)
T ss_pred CCCCCCCCCCc
Confidence 46789999963
No 156
>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=36.00 E-value=35 Score=16.93 Aligned_cols=10 Identities=10% Similarity=0.056 Sum_probs=6.7
Q ss_pred CCCCCCCCCC
Q psy11364 25 LSSSIPGSSK 34 (101)
Q Consensus 25 ~~c~~c~~~~ 34 (101)
+.|+.||..+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 4677777755
No 157
>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=35.25 E-value=25 Score=19.49 Aligned_cols=13 Identities=46% Similarity=1.060 Sum_probs=8.5
Q ss_pred CCcccccCccccC
Q psy11364 79 AFYACSSCSHVSR 91 (101)
Q Consensus 79 kp~~C~~C~k~f~ 91 (101)
.-|.|..|+..+.
T Consensus 89 ~fy~C~~C~~~w~ 101 (104)
T TIGR01384 89 RFYKCTKCGYVWR 101 (104)
T ss_pred EEEEeCCCCCeeE
Confidence 4677777776543
No 158
>PRK05978 hypothetical protein; Provisional
Probab=34.47 E-value=37 Score=20.58 Aligned_cols=11 Identities=18% Similarity=0.048 Sum_probs=5.5
Q ss_pred CCCCCCCCCCC
Q psy11364 24 PLSSSIPGSSK 34 (101)
Q Consensus 24 ~~~c~~c~~~~ 34 (101)
...|+.||++.
T Consensus 33 ~grCP~CG~G~ 43 (148)
T PRK05978 33 RGRCPACGEGK 43 (148)
T ss_pred cCcCCCCCCCc
Confidence 34555555543
No 159
>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=34.23 E-value=25 Score=17.76 Aligned_cols=12 Identities=25% Similarity=0.575 Sum_probs=4.7
Q ss_pred cceecccchhhc
Q psy11364 52 LFATCFVCGKQL 63 (101)
Q Consensus 52 ~~~~C~~c~~~~ 63 (101)
+.+.|..||..+
T Consensus 24 rrhhCr~CG~~v 35 (69)
T PF01363_consen 24 RRHHCRNCGRVV 35 (69)
T ss_dssp -EEE-TTT--EE
T ss_pred eeEccCCCCCEE
Confidence 446666666544
No 160
>KOG2482|consensus
Probab=34.10 E-value=27 Score=24.32 Aligned_cols=23 Identities=26% Similarity=0.580 Sum_probs=21.0
Q ss_pred ceecccchhhcCCHHHHHHHHHh
Q psy11364 53 FATCFVCGKQLSNQYNLRVHMET 75 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h~~~ 75 (101)
.+.|-.|.+.|..+..|..||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 47899999999999999999985
No 161
>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=33.49 E-value=21 Score=20.46 Aligned_cols=26 Identities=23% Similarity=0.692 Sum_probs=15.8
Q ss_pred ceecccchhhcCCHHHHHHHHHhhCCCCcccccCccc
Q psy11364 53 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 89 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~ 89 (101)
...|..|+..|.... ..+.|+.||..
T Consensus 70 ~~~C~~Cg~~~~~~~-----------~~~~CP~Cgs~ 95 (115)
T TIGR00100 70 ECECEDCSEEVSPEI-----------DLYRCPKCHGI 95 (115)
T ss_pred EEEcccCCCEEecCC-----------cCccCcCCcCC
Confidence 367888886664432 13568888753
No 162
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=33.31 E-value=30 Score=23.26 Aligned_cols=30 Identities=30% Similarity=0.656 Sum_probs=16.3
Q ss_pred eecccchhhcCCHHHHHHHHHhhCCCCcccccCccccC
Q psy11364 54 ATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSR 91 (101)
Q Consensus 54 ~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f~ 91 (101)
.+|+.|+...-.+. |.. .-+.|+.||..|.
T Consensus 27 ~~c~~c~~~~~~~~-l~~-------~~~vc~~c~~h~r 56 (285)
T TIGR00515 27 TKCPKCGQVLYTKE-LER-------NLEVCPKCDHHMR 56 (285)
T ss_pred eECCCCcchhhHHH-HHh-------hCCCCCCCCCcCc
Confidence 46777775543322 211 2457777776665
No 163
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=33.10 E-value=18 Score=16.20 Aligned_cols=11 Identities=18% Similarity=0.561 Sum_probs=5.0
Q ss_pred ccccCccccCC
Q psy11364 82 ACSSCSHVSRS 92 (101)
Q Consensus 82 ~C~~C~k~f~~ 92 (101)
.|..|++.|.-
T Consensus 5 ~C~eC~~~f~d 15 (34)
T PF01286_consen 5 KCDECGKPFMD 15 (34)
T ss_dssp E-TTT--EES-
T ss_pred hHhHhCCHHHH
Confidence 57778877764
No 164
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=32.91 E-value=16 Score=16.23 Aligned_cols=11 Identities=27% Similarity=0.549 Sum_probs=6.6
Q ss_pred Ccceecccchh
Q psy11364 51 KLFATCFVCGK 61 (101)
Q Consensus 51 ~~~~~C~~c~~ 61 (101)
...+.|..|+.
T Consensus 20 r~R~vC~~Cg~ 30 (34)
T PF14803_consen 20 RERLVCPACGF 30 (34)
T ss_dssp S-EEEETTTTE
T ss_pred ccceECCCCCC
Confidence 34467877774
No 165
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=32.77 E-value=2.9 Score=23.57 Aligned_cols=9 Identities=44% Similarity=0.730 Sum_probs=4.4
Q ss_pred cceecccch
Q psy11364 52 LFATCFVCG 60 (101)
Q Consensus 52 ~~~~C~~c~ 60 (101)
+.|.|+.|+
T Consensus 21 k~FtCp~Cg 29 (104)
T COG4888 21 KTFTCPRCG 29 (104)
T ss_pred ceEecCccC
Confidence 345555554
No 166
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=32.51 E-value=21 Score=21.32 Aligned_cols=24 Identities=29% Similarity=0.598 Sum_probs=19.3
Q ss_pred cceecccchhhcCCHHHHHHHHHhhCC
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQN 78 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~~ 78 (101)
....|-++|+.|.. |++|+..|-+
T Consensus 75 D~IicLEDGkkfKS---LKRHL~t~~g 98 (148)
T COG4957 75 DYIICLEDGKKFKS---LKRHLTTHYG 98 (148)
T ss_pred CeEEEeccCcchHH---HHHHHhcccC
Confidence 44678899998865 8899999876
No 167
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=32.18 E-value=15 Score=22.13 Aligned_cols=9 Identities=22% Similarity=0.257 Sum_probs=4.3
Q ss_pred CCCCCCCCC
Q psy11364 25 LSSSIPGSS 33 (101)
Q Consensus 25 ~~c~~c~~~ 33 (101)
-.|+.||..
T Consensus 106 ~~cp~c~s~ 114 (146)
T TIGR02159 106 VQCPRCGSA 114 (146)
T ss_pred CcCCCCCCC
Confidence 345555543
No 168
>KOG3497|consensus
Probab=32.07 E-value=22 Score=18.17 Aligned_cols=15 Identities=20% Similarity=0.361 Sum_probs=10.2
Q ss_pred CcccccCccccCChH
Q psy11364 80 FYACSSCSHVSRSRD 94 (101)
Q Consensus 80 p~~C~~C~k~f~~~~ 94 (101)
|..|..|||....++
T Consensus 4 PiRCFtCGKvig~KW 18 (69)
T KOG3497|consen 4 PIRCFTCGKVIGDKW 18 (69)
T ss_pred eeEeeeccccccccH
Confidence 667888887766543
No 169
>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=31.69 E-value=7.2 Score=19.15 Aligned_cols=27 Identities=15% Similarity=0.294 Sum_probs=13.7
Q ss_pred CcceecccchhhcCCHHHHHHHHHhhC
Q psy11364 51 KLFATCFVCGKQLSNQYNLRVHMETHQ 77 (101)
Q Consensus 51 ~~~~~C~~c~~~~~~~~~l~~h~~~h~ 77 (101)
...|.|+.|.+.|-..-.+-.|..+|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-S
T ss_pred CCeEECCCCCCccccCcChhhhccccC
Confidence 356889999888877776665654443
No 170
>KOG0717|consensus
Probab=31.09 E-value=23 Score=25.63 Aligned_cols=20 Identities=25% Similarity=0.639 Sum_probs=15.2
Q ss_pred cccccCccccCChHHHhccc
Q psy11364 81 YACSSCSHVSRSRDALRKHD 100 (101)
Q Consensus 81 ~~C~~C~k~f~~~~~l~~H~ 100 (101)
+-|.+|.|.|.+..+|..|.
T Consensus 293 lyC~vCnKsFKseKq~kNHE 312 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHE 312 (508)
T ss_pred eEEeeccccccchHHHHhhH
Confidence 66888888888887777763
No 171
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=30.76 E-value=44 Score=20.90 Aligned_cols=30 Identities=17% Similarity=0.403 Sum_probs=16.0
Q ss_pred cceecccchhhcCCHHHHHHHHHhhCCCCcccccCccc
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 89 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~ 89 (101)
..|.|+.|...++...... .-|.|+.||..
T Consensus 112 ~~y~C~~~~~r~sfdeA~~--------~~F~Cp~Cg~~ 141 (176)
T COG1675 112 NYYVCPNCHVKYSFDEAME--------LGFTCPKCGED 141 (176)
T ss_pred CceeCCCCCCcccHHHHHH--------hCCCCCCCCch
Confidence 3466766655544433322 13677777754
No 172
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.58 E-value=16 Score=17.75 Aligned_cols=12 Identities=25% Similarity=0.528 Sum_probs=5.9
Q ss_pred ccccCccccCCh
Q psy11364 82 ACSSCSHVSRSR 93 (101)
Q Consensus 82 ~C~~C~k~f~~~ 93 (101)
.|+.|++-|.+.
T Consensus 14 ICpvCqRPFsWR 25 (54)
T COG4338 14 ICPVCQRPFSWR 25 (54)
T ss_pred hhhhhcCchHHH
Confidence 355555555443
No 173
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=30.14 E-value=22 Score=20.89 Aligned_cols=12 Identities=33% Similarity=0.742 Sum_probs=6.8
Q ss_pred CcccccCccccC
Q psy11364 80 FYACSSCSHVSR 91 (101)
Q Consensus 80 p~~C~~C~k~f~ 91 (101)
-|+|..|++.|.
T Consensus 53 RyrC~~C~~tf~ 64 (129)
T COG3677 53 RYKCKSCGSTFT 64 (129)
T ss_pred ccccCCcCccee
Confidence 455666665554
No 174
>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=30.12 E-value=44 Score=22.68 Aligned_cols=41 Identities=20% Similarity=0.244 Sum_probs=18.4
Q ss_pred CCCCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhc
Q psy11364 22 TSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQL 63 (101)
Q Consensus 22 ~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~ 63 (101)
++-+.|+.||..-..-..+++.. .....-..|.|..|+..|
T Consensus 256 t~~~~C~~C~~~~~~~~q~Qtrs-aDEpmT~f~~C~~Cg~~w 296 (299)
T TIGR01385 256 TDLFTCGKCKQKKCTYYQLQTRS-ADEPMTTFVTCEECGNRW 296 (299)
T ss_pred cccccCCCCCCccceEEEecccC-CCCCCeEEEEcCCCCCee
Confidence 34677777775433222222211 111112335677776544
No 175
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.95 E-value=50 Score=21.85 Aligned_cols=32 Identities=19% Similarity=0.215 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCCHHHHH
Q psy11364 23 SPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLR 70 (101)
Q Consensus 23 ~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~~l~ 70 (101)
++-.|+.||. ...+.+.|+.||......-+..
T Consensus 308 tS~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa 339 (364)
T COG0675 308 TSKTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAA 339 (364)
T ss_pred CcccccccCC----------------ccceeEECCCCCCeehhhHHHH
Confidence 4566888886 1246689999998765555433
No 176
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=29.57 E-value=25 Score=20.11 Aligned_cols=27 Identities=15% Similarity=0.306 Sum_probs=15.1
Q ss_pred ceecccchhhcCCHHHHHHHHHhhCCCCcccccCccc
Q psy11364 53 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 89 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~ 89 (101)
...|..|+..|..... ..+.|+.||..
T Consensus 70 ~~~C~~Cg~~~~~~~~----------~~~~CP~Cgs~ 96 (114)
T PRK03681 70 ECWCETCQQYVTLLTQ----------RVRRCPQCHGD 96 (114)
T ss_pred EEEcccCCCeeecCCc----------cCCcCcCcCCC
Confidence 3678888865433211 12558888743
No 177
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=29.56 E-value=39 Score=22.92 Aligned_cols=32 Identities=16% Similarity=0.417 Sum_probs=18.6
Q ss_pred ceecccchhhcCCHHHHHHHHHhhCCCCcccccCccccCC
Q psy11364 53 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRS 92 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f~~ 92 (101)
..+|+.|++..-.+. |.. .-+.|+.||..|.-
T Consensus 38 w~kc~~C~~~~~~~~-l~~-------~~~vcp~c~~h~rl 69 (296)
T CHL00174 38 WVQCENCYGLNYKKF-LKS-------KMNICEQCGYHLKM 69 (296)
T ss_pred eeECCCccchhhHHH-HHH-------cCCCCCCCCCCcCC
Confidence 346888876543322 211 34678888877663
No 178
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=29.43 E-value=34 Score=17.40 Aligned_cols=14 Identities=21% Similarity=0.510 Sum_probs=8.5
Q ss_pred CcccccCccccCCh
Q psy11364 80 FYACSSCSHVSRSR 93 (101)
Q Consensus 80 p~~C~~C~k~f~~~ 93 (101)
|..|..||+.....
T Consensus 4 PVRCFTCGkvi~~~ 17 (60)
T PF01194_consen 4 PVRCFTCGKVIGNK 17 (60)
T ss_dssp SSS-STTTSBTCGH
T ss_pred ceecCCCCCChhHh
Confidence 66777787765543
No 179
>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=28.65 E-value=51 Score=18.93 Aligned_cols=12 Identities=8% Similarity=-0.316 Sum_probs=5.5
Q ss_pred CCCCCCCCCCCc
Q psy11364 24 PLSSSIPGSSKT 35 (101)
Q Consensus 24 ~~~c~~c~~~~~ 35 (101)
-+.|+.|+..|.
T Consensus 19 ~~iCpeC~~EW~ 30 (109)
T TIGR00686 19 QLICPSCLYEWN 30 (109)
T ss_pred eeECcccccccc
Confidence 344444444443
No 180
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=28.65 E-value=32 Score=16.54 Aligned_cols=27 Identities=22% Similarity=0.288 Sum_probs=15.4
Q ss_pred CCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhcCC
Q psy11364 26 SSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSN 65 (101)
Q Consensus 26 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~ 65 (101)
.|..|++.|.. ..+.+.|..||+.+-.
T Consensus 4 ~C~~C~~~F~~-------------~~rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 4 SCMGCGKPFTL-------------TRRRHHCRNCGRIFCS 30 (57)
T ss_pred cCcccCccccC-------------CccccccCcCcCCcCh
Confidence 46667766643 1233567777766544
No 181
>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=28.56 E-value=52 Score=23.86 Aligned_cols=29 Identities=34% Similarity=0.468 Sum_probs=24.7
Q ss_pred CCcceecccchhhcCCHHHHHHHHH-hhCC
Q psy11364 50 SKLFATCFVCGKQLSNQYNLRVHME-THQN 78 (101)
Q Consensus 50 ~~~~~~C~~c~~~~~~~~~l~~h~~-~h~~ 78 (101)
..+.+.|+.|.+.|.....+..|+. .|.+
T Consensus 54 sWrFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 54 SWRFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred ceeEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 3677899999999999999999987 4664
No 182
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=28.47 E-value=8.6 Score=21.25 Aligned_cols=10 Identities=30% Similarity=0.803 Sum_probs=5.6
Q ss_pred eecccchhhc
Q psy11364 54 ATCFVCGKQL 63 (101)
Q Consensus 54 ~~C~~c~~~~ 63 (101)
|.|..|++.|
T Consensus 55 W~C~~C~~~~ 64 (90)
T PRK03976 55 WECRKCGAKF 64 (90)
T ss_pred EEcCCCCCEE
Confidence 5566666543
No 183
>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=28.12 E-value=23 Score=16.06 Aligned_cols=11 Identities=36% Similarity=1.274 Sum_probs=5.3
Q ss_pred CCcccccCccc
Q psy11364 79 AFYACSSCSHV 89 (101)
Q Consensus 79 kp~~C~~C~k~ 89 (101)
+-|+|..||..
T Consensus 5 ~~YkC~~CGni 15 (36)
T PF06397_consen 5 EFYKCEHCGNI 15 (36)
T ss_dssp EEEE-TTT--E
T ss_pred cEEEccCCCCE
Confidence 45777777754
No 184
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=28.00 E-value=5.4 Score=17.94 Aligned_cols=12 Identities=25% Similarity=0.778 Sum_probs=5.0
Q ss_pred CcccccCccccC
Q psy11364 80 FYACSSCSHVSR 91 (101)
Q Consensus 80 p~~C~~C~k~f~ 91 (101)
+..|..||-.++
T Consensus 21 ~isC~~CGPr~~ 32 (35)
T PF07503_consen 21 FISCTNCGPRYS 32 (35)
T ss_dssp T--BTTCC-SCC
T ss_pred CccCCCCCCCEE
Confidence 445666665543
No 185
>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=27.74 E-value=20 Score=23.95 Aligned_cols=11 Identities=18% Similarity=0.461 Sum_probs=6.7
Q ss_pred CCcccccCccc
Q psy11364 79 AFYACSSCSHV 89 (101)
Q Consensus 79 kp~~C~~C~k~ 89 (101)
+|+.|+.||.-
T Consensus 208 k~~PCPKCg~e 218 (314)
T PF06524_consen 208 KPIPCPKCGYE 218 (314)
T ss_pred CCCCCCCCCCc
Confidence 56666666643
No 186
>KOG3507|consensus
Probab=26.98 E-value=36 Score=17.28 Aligned_cols=13 Identities=23% Similarity=0.531 Sum_probs=9.4
Q ss_pred Ccceecccchhhc
Q psy11364 51 KLFATCFVCGKQL 63 (101)
Q Consensus 51 ~~~~~C~~c~~~~ 63 (101)
..++.|.+||...
T Consensus 35 ~D~irCReCG~RI 47 (62)
T KOG3507|consen 35 GDVIRCRECGYRI 47 (62)
T ss_pred CCcEehhhcchHH
Confidence 4568899998644
No 187
>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 PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=26.58 E-value=76 Score=14.31 Aligned_cols=20 Identities=20% Similarity=0.298 Sum_probs=12.9
Q ss_pred cceecccchhhcCCHHHHHH
Q psy11364 52 LFATCFVCGKQLSNQYNLRV 71 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~ 71 (101)
....|..|+-.+.....+..
T Consensus 18 ~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 18 EIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEEECCCCCeEEccHHHHHH
Confidence 34667777777766666543
No 189
>PRK04351 hypothetical protein; Provisional
Probab=25.98 E-value=24 Score=21.30 Aligned_cols=35 Identities=20% Similarity=0.456 Sum_probs=22.7
Q ss_pred cceecccchhhcCCHHHHHHHHHhhCCCCcccccCccccCCh
Q psy11364 52 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRSR 93 (101)
Q Consensus 52 ~~~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f~~~ 93 (101)
-.|.|..|+..+.. + +.+...-|.|..|+..+...
T Consensus 111 y~Y~C~~Cg~~~~r------~-Rr~n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 111 YLYECQSCGQQYLR------K-RRINTKRYRCGKCRGKLKLI 145 (149)
T ss_pred EEEECCCCCCEeee------e-eecCCCcEEeCCCCcEeeec
Confidence 34889889866533 2 22333679999998766543
No 190
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=25.81 E-value=46 Score=22.47 Aligned_cols=30 Identities=30% Similarity=0.698 Sum_probs=16.0
Q ss_pred eecccchhhcCCHHHHHHHHHhhCCCCcccccCccccC
Q psy11364 54 ATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSR 91 (101)
Q Consensus 54 ~~C~~c~~~~~~~~~l~~h~~~h~~kp~~C~~C~k~f~ 91 (101)
.+|+.|+...-.+. |.. .-+.|+.||..|.
T Consensus 28 ~~c~~c~~~~~~~~-l~~-------~~~vc~~c~~h~r 57 (292)
T PRK05654 28 TKCPSCGQVLYRKE-LEA-------NLNVCPKCGHHMR 57 (292)
T ss_pred eECCCccchhhHHH-HHh-------cCCCCCCCCCCee
Confidence 46777765432222 111 2357777777665
No 191
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=25.79 E-value=49 Score=16.51 Aligned_cols=12 Identities=25% Similarity=0.487 Sum_probs=8.6
Q ss_pred Ccceecccchhh
Q psy11364 51 KLFATCFVCGKQ 62 (101)
Q Consensus 51 ~~~~~C~~c~~~ 62 (101)
...|.|+.||-.
T Consensus 12 ~v~~~Cp~cGip 23 (55)
T PF13824_consen 12 HVNFECPDCGIP 23 (55)
T ss_pred ccCCcCCCCCCc
Confidence 455889888853
No 192
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=25.49 E-value=91 Score=23.68 Aligned_cols=11 Identities=18% Similarity=-0.076 Sum_probs=6.6
Q ss_pred CCCCCCCCCCC
Q psy11364 24 PLSSSIPGSSK 34 (101)
Q Consensus 24 ~~~c~~c~~~~ 34 (101)
.-.|+.||...
T Consensus 15 akFC~~CG~~l 25 (645)
T PRK14559 15 NRFCQKCGTSL 25 (645)
T ss_pred CccccccCCCC
Confidence 44566776654
No 193
>COG1773 Rubredoxin [Energy production and conversion]
Probab=25.03 E-value=31 Score=17.22 Aligned_cols=10 Identities=40% Similarity=0.913 Sum_probs=5.3
Q ss_pred cccccCcccc
Q psy11364 81 YACSSCSHVS 90 (101)
Q Consensus 81 ~~C~~C~k~f 90 (101)
|+|..||..|
T Consensus 4 ~~C~~CG~vY 13 (55)
T COG1773 4 WRCSVCGYVY 13 (55)
T ss_pred eEecCCceEe
Confidence 4555555444
No 194
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=24.64 E-value=50 Score=17.94 Aligned_cols=35 Identities=9% Similarity=-0.017 Sum_probs=20.7
Q ss_pred CCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhhc
Q psy11364 26 SSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQL 63 (101)
Q Consensus 26 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~ 63 (101)
.|-.||...+....+... +. ...+.|-|..|.-++
T Consensus 2 ~C~HCg~~~p~~~~~~~~--~~-g~~~~FCC~GC~~V~ 36 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVE--ID-GEERPFCCPGCQAVY 36 (88)
T ss_pred CCCCCCCCCCCCCCeeee--eC-CCccccccHHHHHHH
Confidence 477788777544333222 11 235788999997554
No 195
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=24.54 E-value=2e+02 Score=23.97 Aligned_cols=10 Identities=30% Similarity=0.737 Sum_probs=6.4
Q ss_pred ceecccchhh
Q psy11364 53 FATCFVCGKQ 62 (101)
Q Consensus 53 ~~~C~~c~~~ 62 (101)
++.|+.||..
T Consensus 692 vy~CPsCGae 701 (1337)
T PRK14714 692 VYVCPDCGAE 701 (1337)
T ss_pred ceeCccCCCc
Confidence 4567777754
No 196
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=24.34 E-value=25 Score=22.34 Aligned_cols=9 Identities=33% Similarity=0.940 Sum_probs=0.0
Q ss_pred CCcccccCc
Q psy11364 79 AFYACSSCS 87 (101)
Q Consensus 79 kp~~C~~C~ 87 (101)
+-|.|.+||
T Consensus 100 ~ey~CEICG 108 (196)
T PF11931_consen 100 VEYKCEICG 108 (196)
T ss_dssp ---------
T ss_pred CeeeeEeCC
Confidence 667777776
No 197
>PF10621 FpoO: F420H2 dehydrogenase subunit FpoO ; InterPro: IPR018288 This entry represents the FpoO subunit of membrane-bound multi-subunit F420H2 dehydrogenase, which oxidises the reduced coenzyme F420H2 to coenzyme F420 and feeds the electrons via an FeS cluster into an energy-conserving electron transport chain [, ]. This enzyme plays a role in the methanogenic pathway in methanogenic archaea. Reduced coenzyme F420H2 is the major cytoplasmic electron carrier of methanogens and a reversible hydride donor, much like NADH []. F420H2 + COB-S-S-CoM = F420 + CoM-SH + CoB-SH Where CoB-S-S-CoM (the heterosulphide of 2-mercaptoethanesulphonate and 7-mercaptoheptanoylthreonine phosphate) is the terminal electron acceptor of the methanogenic pathway, and is reduced with the concomitant generation of a transmembrane proton potential and ATP synthesis. The FpoO subunit of F420H2 dehydrogenase probably participates in the reduction of methanophenazine, where it acts as a special mechanism for the reduction of the methanogenic cofactor [].
Probab=24.25 E-value=39 Score=19.47 Aligned_cols=60 Identities=10% Similarity=0.077 Sum_probs=29.3
Q ss_pred CCCCCCCCccCCCCCC---CCCCCCCCCcce--ecccchhhcCCHHHHHHHHHhhCC-CCcccccCccc
Q psy11364 27 SSIPGSSKTKASGSGT---TGGSSNHSKLFA--TCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHV 89 (101)
Q Consensus 27 c~~c~~~~~~~~~~~~---~~~~~~~~~~~~--~C~~c~~~~~~~~~l~~h~~~h~~-kp~~C~~C~k~ 89 (101)
|+.||.+.++--+... ......+ +-.| .|..|-... ......+-+.+.. +.=+|..||+.
T Consensus 4 CdLCg~~~Pt~~PvrV~~Pr~~~~yP-eGvwKGLC~~CL~sa--~~ty~e~~~~~~s~~~gKC~LCG~k 69 (119)
T PF10621_consen 4 CDLCGRAIPTVCPVRVFAPRLTLAYP-EGVWKGLCETCLDSA--EKTYQEVNENESSCRSGKCDLCGKK 69 (119)
T ss_pred cchhcCcCCceeEEEeecchhhccCc-chHHHhhHHHHHHHH--HHHHHHHhcccccccccceeccCCc
Confidence 6677776655433221 1111111 2223 466665432 2333444444555 67788999863
No 198
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=24.20 E-value=50 Score=20.48 Aligned_cols=18 Identities=17% Similarity=0.451 Sum_probs=14.5
Q ss_pred CCcccccCccccCChHHH
Q psy11364 79 AFYACSSCSHVSRSRDAL 96 (101)
Q Consensus 79 kp~~C~~C~k~f~~~~~l 96 (101)
....|..||+.|.....+
T Consensus 113 ~~~~C~~Cg~~f~~~k~i 130 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTV 130 (181)
T ss_pred ccCcCcccCCccCcHhHH
Confidence 688899999999866444
No 199
>KOG0978|consensus
Probab=24.06 E-value=35 Score=25.99 Aligned_cols=21 Identities=24% Similarity=0.436 Sum_probs=16.5
Q ss_pred CCcccccCccccCChHHHhcc
Q psy11364 79 AFYACSSCSHVSRSRDALRKH 99 (101)
Q Consensus 79 kp~~C~~C~k~f~~~~~l~~H 99 (101)
+.=+||.|+.+|...+-+.-|
T Consensus 677 RqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred hcCCCCCCCCCCCcccccccC
Confidence 556899999999987766554
No 200
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=23.97 E-value=30 Score=20.50 Aligned_cols=32 Identities=22% Similarity=0.403 Sum_probs=18.1
Q ss_pred ceecccchhhcCCHHHHHHHHHhhCC-CCcccccCccccC
Q psy11364 53 FATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVSR 91 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~~l~~h~~~h~~-kp~~C~~C~k~f~ 91 (101)
.|.|..|+..+. ++. -+.. .-|.|..|+..+.
T Consensus 112 ~y~C~~C~~~~~------~~r-r~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRYL------RVR-RSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCCc------eEc-cccCcceEEcCCCCCEEE
Confidence 477877876543 121 1222 4577887876543
No 201
>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=23.87 E-value=27 Score=16.19 Aligned_cols=10 Identities=30% Similarity=0.753 Sum_probs=5.1
Q ss_pred ceecccchhh
Q psy11364 53 FATCFVCGKQ 62 (101)
Q Consensus 53 ~~~C~~c~~~ 62 (101)
+-.|+.|+..
T Consensus 29 ~~~CpYCg~~ 38 (40)
T PF10276_consen 29 PVVCPYCGTR 38 (40)
T ss_dssp EEEETTTTEE
T ss_pred eEECCCCCCE
Confidence 3455555543
No 202
>PRK10220 hypothetical protein; Provisional
Probab=23.27 E-value=1.1e+02 Score=17.57 Aligned_cols=14 Identities=7% Similarity=-0.213 Sum_probs=7.6
Q ss_pred CCCCCCCCCCCccC
Q psy11364 24 PLSSSIPGSSKTKA 37 (101)
Q Consensus 24 ~~~c~~c~~~~~~~ 37 (101)
-|.|+.|+..|...
T Consensus 20 ~~vCpeC~hEW~~~ 33 (111)
T PRK10220 20 MYICPECAHEWNDA 33 (111)
T ss_pred eEECCcccCcCCcc
Confidence 45566666555444
No 203
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=23.05 E-value=65 Score=15.56 Aligned_cols=15 Identities=20% Similarity=0.550 Sum_probs=9.8
Q ss_pred ceecccchhhcCCHH
Q psy11364 53 FATCFVCGKQLSNQY 67 (101)
Q Consensus 53 ~~~C~~c~~~~~~~~ 67 (101)
-+.|..|+..+...-
T Consensus 28 ~W~C~~Cgh~w~~~v 42 (55)
T PF14311_consen 28 WWKCPKCGHEWKASV 42 (55)
T ss_pred EEECCCCCCeeEccH
Confidence 367888876665543
No 204
>PF14369 zf-RING_3: zinc-finger
Probab=22.59 E-value=49 Score=14.69 Aligned_cols=10 Identities=0% Similarity=-0.257 Sum_probs=8.2
Q ss_pred CCCCCCCCCc
Q psy11364 26 SSSIPGSSKT 35 (101)
Q Consensus 26 ~c~~c~~~~~ 35 (101)
.|+.|+.+|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 5999998874
No 205
>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=22.56 E-value=33 Score=16.43 Aligned_cols=10 Identities=40% Similarity=0.989 Sum_probs=5.2
Q ss_pred cccccCcccc
Q psy11364 81 YACSSCSHVS 90 (101)
Q Consensus 81 ~~C~~C~k~f 90 (101)
|.|..||..+
T Consensus 2 y~C~~CgyvY 11 (47)
T PF00301_consen 2 YQCPVCGYVY 11 (47)
T ss_dssp EEETTTSBEE
T ss_pred cCCCCCCEEE
Confidence 4555665443
No 206
>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=22.37 E-value=30 Score=16.36 Aligned_cols=8 Identities=25% Similarity=0.156 Sum_probs=5.0
Q ss_pred CCCCCCCC
Q psy11364 27 SSIPGSSK 34 (101)
Q Consensus 27 c~~c~~~~ 34 (101)
|+.||..-
T Consensus 2 CP~Cg~~a 9 (47)
T PF04606_consen 2 CPHCGSKA 9 (47)
T ss_pred cCCCCCee
Confidence 67777643
No 207
>KOG1280|consensus
Probab=22.27 E-value=78 Score=22.15 Aligned_cols=37 Identities=22% Similarity=0.375 Sum_probs=25.1
Q ss_pred CcceecccchhhcCCHHHHHHHHH-hhCC--CCcccccCc
Q psy11364 51 KLFATCFVCGKQLSNQYNLRVHME-THQN--AFYACSSCS 87 (101)
Q Consensus 51 ~~~~~C~~c~~~~~~~~~l~~h~~-~h~~--kp~~C~~C~ 87 (101)
+.-|.|+.|++.-.....+..|.. .|.. -...|+.|+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 346889999987777777888864 5655 234456664
No 208
>KOG0782|consensus
Probab=22.23 E-value=23 Score=26.58 Aligned_cols=17 Identities=6% Similarity=-0.259 Sum_probs=9.3
Q ss_pred CCCCCCCCCCCccCCCC
Q psy11364 24 PLSSSIPGSSKTKASGS 40 (101)
Q Consensus 24 ~~~c~~c~~~~~~~~~~ 40 (101)
.-.|..||++|.++-.+
T Consensus 253 eGkC~~CgKgFQQKf~F 269 (1004)
T KOG0782|consen 253 EGKCNTCGKGFQQKFFF 269 (1004)
T ss_pred ccccchhhhhhhhheee
Confidence 44566666666555443
No 209
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=21.68 E-value=42 Score=17.22 Aligned_cols=13 Identities=23% Similarity=0.473 Sum_probs=8.6
Q ss_pred CcccccCccccCC
Q psy11364 80 FYACSSCSHVSRS 92 (101)
Q Consensus 80 p~~C~~C~k~f~~ 92 (101)
|..|..||+....
T Consensus 4 PvRCFTCGkvi~~ 16 (62)
T PRK04016 4 PVRCFTCGKVIAE 16 (62)
T ss_pred CeEecCCCCChHH
Confidence 6677777776544
No 210
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.58 E-value=29 Score=18.59 Aligned_cols=11 Identities=27% Similarity=0.803 Sum_probs=6.9
Q ss_pred CcccccCcccc
Q psy11364 80 FYACSSCSHVS 90 (101)
Q Consensus 80 p~~C~~C~k~f 90 (101)
.|+|..||..|
T Consensus 12 ~Y~c~~cg~~~ 22 (82)
T COG2331 12 SYECTECGNRF 22 (82)
T ss_pred EEeecccchHH
Confidence 36777776554
No 211
>KOG4124|consensus
Probab=21.31 E-value=18 Score=25.21 Aligned_cols=21 Identities=29% Similarity=0.616 Sum_probs=15.9
Q ss_pred CCcccccCccccCChHHHhcc
Q psy11364 79 AFYACSSCSHVSRSRDALRKH 99 (101)
Q Consensus 79 kp~~C~~C~k~f~~~~~l~~H 99 (101)
|||+|++|.+++.-...|..|
T Consensus 397 k~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 397 KPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred CcccChhhhhhhccCCCCCce
Confidence 899999999887766555443
No 212
>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=21.25 E-value=34 Score=15.35 Aligned_cols=9 Identities=22% Similarity=0.922 Sum_probs=4.8
Q ss_pred ccccCcccc
Q psy11364 82 ACSSCSHVS 90 (101)
Q Consensus 82 ~C~~C~k~f 90 (101)
.|+.||+.|
T Consensus 3 ~C~~Cg~~Y 11 (36)
T PF05191_consen 3 ICPKCGRIY 11 (36)
T ss_dssp EETTTTEEE
T ss_pred CcCCCCCcc
Confidence 355566554
No 213
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=20.62 E-value=54 Score=15.03 Aligned_cols=10 Identities=20% Similarity=0.471 Sum_probs=6.8
Q ss_pred CcccccCccc
Q psy11364 80 FYACSSCSHV 89 (101)
Q Consensus 80 p~~C~~C~k~ 89 (101)
|..|+.||..
T Consensus 2 ~~~Cp~Cg~~ 11 (47)
T PF14690_consen 2 PPRCPHCGSP 11 (47)
T ss_pred CccCCCcCCC
Confidence 5678888743
No 214
>PRK06260 threonine synthase; Validated
Probab=20.56 E-value=54 Score=22.89 Aligned_cols=25 Identities=24% Similarity=0.372 Sum_probs=15.1
Q ss_pred CCCCCCCCCCccCCCCCCCCCCCCCCCcceecccchhh
Q psy11364 25 LSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQ 62 (101)
Q Consensus 25 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~ 62 (101)
+.|..||..+.. ....+.|+.|+-.
T Consensus 4 ~~C~~cg~~~~~-------------~~~~~~Cp~cg~~ 28 (397)
T PRK06260 4 LKCIECGKEYDP-------------DEIIYTCPECGGL 28 (397)
T ss_pred EEECCCCCCCCC-------------CCccccCCCCCCe
Confidence 567788865521 1234678888754
No 215
>PF12773 DZR: Double zinc ribbon
Probab=20.47 E-value=98 Score=14.39 Aligned_cols=6 Identities=33% Similarity=1.326 Sum_probs=2.4
Q ss_pred ccccCc
Q psy11364 82 ACSSCS 87 (101)
Q Consensus 82 ~C~~C~ 87 (101)
.|+.||
T Consensus 31 ~C~~Cg 36 (50)
T PF12773_consen 31 ICPNCG 36 (50)
T ss_pred CCcCCc
Confidence 344443
No 216
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=20.04 E-value=50 Score=14.97 Aligned_cols=14 Identities=14% Similarity=0.337 Sum_probs=7.2
Q ss_pred ccccCccccCChHH
Q psy11364 82 ACSSCSHVSRSRDA 95 (101)
Q Consensus 82 ~C~~C~k~f~~~~~ 95 (101)
.|+-|++.|-+.+.
T Consensus 4 ~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 4 LCPRCGKGFHWASE 17 (36)
T ss_dssp C-TTTSSSCS-TTT
T ss_pred cCcccCCCcchhhh
Confidence 46667776655443
Done!