Query psy3500
Match_columns 98
No_of_seqs 115 out of 1864
Neff 11.5
Searched_HMMs 46136
Date Fri Aug 16 18:18:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3500.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3500hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 2.4E-29 5.1E-34 140.8 5.7 94 2-97 131-238 (279)
2 KOG2462|consensus 99.9 4.4E-28 9.4E-33 135.8 4.7 95 1-95 161-264 (279)
3 KOG3576|consensus 99.7 6.4E-18 1.4E-22 92.0 1.0 79 17-95 116-194 (267)
4 KOG3576|consensus 99.7 1.4E-17 3E-22 90.7 1.9 96 2-97 118-235 (267)
5 KOG3623|consensus 99.7 1.4E-17 3.1E-22 104.1 1.2 79 16-94 892-970 (1007)
6 KOG1074|consensus 99.6 6.1E-17 1.3E-21 102.3 -0.1 80 18-97 605-691 (958)
7 KOG3608|consensus 99.6 5.2E-16 1.1E-20 90.6 1.9 92 4-97 210-315 (467)
8 KOG3623|consensus 99.5 2.4E-15 5.2E-20 94.4 1.7 79 17-95 239-330 (1007)
9 PHA00733 hypothetical protein 99.3 1.2E-12 2.7E-17 68.0 3.6 80 16-97 38-122 (128)
10 KOG3608|consensus 99.3 8.9E-13 1.9E-17 77.4 2.3 84 11-95 285-373 (467)
11 KOG1074|consensus 99.3 3.2E-13 7E-18 86.0 0.2 53 45-97 604-656 (958)
12 PLN03086 PRLI-interacting fact 99.2 8.7E-11 1.9E-15 73.4 7.2 74 7-85 441-515 (567)
13 PHA02768 hypothetical protein; 99.2 7.4E-12 1.6E-16 55.2 1.4 39 19-59 6-44 (55)
14 PHA02768 hypothetical protein; 99.1 3E-11 6.5E-16 53.3 2.1 43 46-90 5-47 (55)
15 PLN03086 PRLI-interacting fact 99.1 5.3E-10 1.2E-14 70.0 7.6 89 2-94 454-560 (567)
16 PHA00733 hypothetical protein 99.1 7.8E-11 1.7E-15 61.3 3.4 53 15-69 70-122 (128)
17 PF13465 zf-H2C2_2: Zinc-finge 99.1 1.1E-10 2.4E-15 44.4 2.7 24 62-85 2-25 (26)
18 PF13465 zf-H2C2_2: Zinc-finge 98.9 1.8E-09 3.9E-14 41.0 2.8 25 33-57 1-25 (26)
19 KOG3993|consensus 98.8 8E-10 1.7E-14 66.4 0.2 24 74-97 356-379 (500)
20 PHA00616 hypothetical protein 98.7 9.6E-09 2.1E-13 43.4 1.4 34 18-51 1-34 (44)
21 PHA00732 hypothetical protein 98.6 6.3E-08 1.4E-12 46.3 2.5 45 18-68 1-46 (79)
22 PF00096 zf-C2H2: Zinc finger, 98.5 1E-07 2.2E-12 35.0 2.3 23 75-97 1-23 (23)
23 PHA00616 hypothetical protein 98.5 5E-08 1.1E-12 41.2 1.2 34 46-79 1-34 (44)
24 PHA00732 hypothetical protein 98.5 2.8E-07 6E-12 44.2 3.2 44 46-95 1-45 (79)
25 PF13894 zf-C2H2_4: C2H2-type 98.3 1.3E-06 2.8E-11 32.1 2.5 24 75-98 1-24 (24)
26 PF13912 zf-C2H2_6: C2H2-type 98.3 9.7E-07 2.1E-11 33.6 2.2 24 74-97 1-24 (27)
27 PF00096 zf-C2H2: Zinc finger, 98.3 1.1E-06 2.3E-11 32.2 2.2 22 19-40 1-22 (23)
28 PF05605 zf-Di19: Drought indu 98.2 3.7E-06 8.1E-11 37.4 3.8 46 47-95 3-50 (54)
29 PF05605 zf-Di19: Drought indu 98.2 8E-06 1.7E-10 36.4 4.4 49 18-69 2-52 (54)
30 PF12756 zf-C2H2_2: C2H2 type 98.1 3E-06 6.6E-11 42.1 3.0 72 20-97 1-73 (100)
31 PF13894 zf-C2H2_4: C2H2-type 97.9 1.9E-05 4.2E-10 28.8 2.5 23 19-41 1-23 (24)
32 smart00355 ZnF_C2H2 zinc finge 97.9 1.7E-05 3.6E-10 29.4 2.1 23 75-97 1-23 (26)
33 PF13912 zf-C2H2_6: C2H2-type 97.8 1.8E-05 3.9E-10 30.0 1.8 21 19-39 2-22 (27)
34 PF09237 GAGA: GAGA factor; I 97.7 5.8E-05 1.3E-09 32.8 2.6 31 43-73 21-51 (54)
35 KOG3993|consensus 97.7 5E-06 1.1E-10 50.7 -1.2 51 47-97 268-318 (500)
36 smart00355 ZnF_C2H2 zinc finge 97.6 0.00013 2.9E-09 26.8 2.6 23 19-41 1-23 (26)
37 PRK04860 hypothetical protein; 97.6 0.00011 2.4E-09 39.9 3.2 38 46-87 119-156 (160)
38 PF12874 zf-met: Zinc-finger o 97.5 0.00012 2.7E-09 27.1 2.1 23 75-97 1-23 (25)
39 COG5189 SFP1 Putative transcri 97.5 4.2E-05 9E-10 45.4 0.7 52 44-95 347-419 (423)
40 PF09237 GAGA: GAGA factor; I 97.3 0.00066 1.4E-08 29.6 3.5 33 14-46 20-52 (54)
41 PRK04860 hypothetical protein; 97.2 0.00038 8.3E-09 37.8 2.5 40 17-60 118-157 (160)
42 PF12874 zf-met: Zinc-finger o 97.2 0.00031 6.7E-09 25.9 1.5 21 19-39 1-21 (25)
43 PF12171 zf-C2H2_jaz: Zinc-fin 97.1 0.00021 4.5E-09 27.1 0.6 22 75-96 2-23 (27)
44 COG5189 SFP1 Putative transcri 96.9 0.00035 7.7E-09 41.6 0.6 53 15-67 346-419 (423)
45 PF13909 zf-H2C2_5: C2H2-type 96.8 0.0024 5.1E-08 23.3 2.4 22 19-41 1-22 (24)
46 PF13913 zf-C2HC_2: zinc-finge 96.5 0.0034 7.4E-08 23.3 2.0 21 75-96 3-23 (25)
47 PRK14890 putative Zn-ribbon RN 96.4 0.0052 1.1E-07 27.6 2.6 9 73-81 47-55 (59)
48 COG2888 Predicted Zn-ribbon RN 96.3 0.0075 1.6E-07 27.1 2.6 32 45-81 26-57 (61)
49 PF12756 zf-C2H2_2: C2H2 type 96.0 0.011 2.4E-07 29.1 3.0 24 46-69 50-73 (100)
50 KOG2231|consensus 96.0 0.018 3.9E-07 38.0 4.3 92 2-96 100-204 (669)
51 smart00451 ZnF_U1 U1-like zinc 95.9 0.01 2.2E-07 23.6 2.1 22 74-95 3-24 (35)
52 PRK00398 rpoP DNA-directed RNA 95.8 0.0065 1.4E-07 26.0 1.3 27 2-28 4-31 (46)
53 cd00350 rubredoxin_like Rubred 95.7 0.0085 1.8E-07 23.8 1.5 24 2-26 2-25 (33)
54 smart00659 RPOLCX RNA polymera 95.6 0.011 2.3E-07 25.2 1.6 26 2-27 3-28 (44)
55 cd00729 rubredoxin_SM Rubredox 95.4 0.0093 2E-07 23.9 1.1 24 2-26 3-26 (34)
56 PF07754 DUF1610: Domain of un 95.2 0.031 6.7E-07 20.5 2.0 22 4-25 1-23 (24)
57 PF10571 UPF0547: Uncharacteri 95.1 0.027 5.9E-07 21.1 1.8 22 4-28 3-24 (26)
58 PF13719 zinc_ribbon_5: zinc-r 94.9 0.043 9.2E-07 22.3 2.3 33 48-85 4-36 (37)
59 PF03604 DNA_RNApol_7kD: DNA d 94.8 0.024 5.3E-07 22.4 1.4 27 2-28 1-27 (32)
60 TIGR00622 ssl1 transcription f 94.5 0.12 2.6E-06 26.6 3.8 90 2-97 2-104 (112)
61 PF09538 FYDLN_acid: Protein o 94.4 0.041 8.8E-07 28.1 2.0 34 15-59 6-39 (108)
62 COG5048 FOG: Zn-finger [Genera 94.2 0.0098 2.1E-07 36.6 -0.5 62 17-78 288-355 (467)
63 COG1592 Rubrerythrin [Energy p 94.1 0.034 7.4E-07 30.5 1.5 11 43-53 146-156 (166)
64 PF13717 zinc_ribbon_4: zinc-r 93.8 0.11 2.4E-06 21.0 2.4 33 47-84 3-35 (36)
65 TIGR02098 MJ0042_CXXC MJ0042 f 93.7 0.11 2.3E-06 21.1 2.3 34 47-85 3-36 (38)
66 KOG1146|consensus 93.5 0.028 6E-07 39.7 0.5 75 17-95 464-539 (1406)
67 PF07649 C1_3: C1-like domain; 93.4 0.062 1.3E-06 20.7 1.3 24 2-27 1-24 (30)
68 COG5048 FOG: Zn-finger [Genera 93.1 0.016 3.5E-07 35.6 -0.9 53 45-97 288-346 (467)
69 PF09723 Zn-ribbon_8: Zinc rib 92.8 0.068 1.5E-06 22.4 1.1 10 19-28 6-15 (42)
70 COG1996 RPC10 DNA-directed RNA 92.8 0.059 1.3E-06 23.4 0.8 11 18-28 6-16 (49)
71 PRK09678 DNA-binding transcrip 92.7 0.093 2E-06 24.8 1.5 30 1-30 1-41 (72)
72 TIGR02300 FYDLN_acid conserved 92.5 0.13 2.8E-06 27.0 2.0 26 4-29 12-37 (129)
73 TIGR00373 conserved hypothetic 92.5 0.23 4.9E-06 27.2 3.1 34 43-85 106-139 (158)
74 KOG2186|consensus 92.5 0.13 2.8E-06 30.1 2.2 49 19-70 4-52 (276)
75 COG4049 Uncharacterized protei 92.3 0.095 2.1E-06 23.3 1.2 25 70-94 13-37 (65)
76 PF03107 C1_2: C1 domain; Int 92.2 0.2 4.4E-06 19.2 2.0 22 2-25 1-22 (30)
77 TIGR02605 CxxC_CxxC_SSSS putat 91.7 0.11 2.3E-06 22.7 1.1 12 18-29 5-16 (52)
78 smart00834 CxxC_CXXC_SSSS Puta 91.5 0.12 2.7E-06 21.1 1.1 10 19-28 6-15 (41)
79 PHA00626 hypothetical protein 91.4 0.32 6.9E-06 21.7 2.3 13 17-29 22-34 (59)
80 smart00661 RPOL9 RNA polymeras 91.4 0.25 5.5E-06 21.4 2.1 25 4-28 3-30 (52)
81 PF09986 DUF2225: Uncharacteri 91.1 0.053 1.2E-06 31.0 -0.3 12 75-86 49-60 (214)
82 COG1645 Uncharacterized Zn-fin 91.0 0.12 2.7E-06 27.2 1.0 25 2-28 29-54 (131)
83 KOG2893|consensus 90.9 0.087 1.9E-06 30.7 0.4 43 19-65 11-53 (341)
84 TIGR01206 lysW lysine biosynth 90.9 0.25 5.5E-06 22.0 1.8 26 2-27 3-31 (54)
85 PRK06266 transcription initiat 90.7 0.38 8.3E-06 26.8 2.8 33 44-85 115-147 (178)
86 PF13240 zinc_ribbon_2: zinc-r 90.5 0.27 5.8E-06 17.8 1.5 20 4-26 2-21 (23)
87 cd00730 rubredoxin Rubredoxin; 90.5 0.31 6.7E-06 21.3 1.9 13 1-13 1-13 (50)
88 KOG2186|consensus 90.3 0.3 6.4E-06 28.7 2.2 46 2-48 4-58 (276)
89 PRK03824 hypA hydrogenase nick 90.2 0.17 3.7E-06 26.9 1.1 17 15-31 67-83 (135)
90 PF12773 DZR: Double zinc ribb 90.0 0.48 1E-05 20.3 2.3 23 4-29 1-23 (50)
91 COG3357 Predicted transcriptio 89.9 0.25 5.4E-06 24.4 1.4 11 18-28 58-68 (97)
92 PRK04023 DNA polymerase II lar 89.9 0.65 1.4E-05 32.7 3.7 21 2-27 627-647 (1121)
93 PRK00432 30S ribosomal protein 89.6 0.33 7.3E-06 21.2 1.6 11 46-56 37-47 (50)
94 PF12760 Zn_Tnp_IS1595: Transp 89.5 0.4 8.6E-06 20.4 1.8 24 2-25 19-44 (46)
95 PF06524 NOA36: NOA36 protein; 89.4 0.22 4.9E-06 29.4 1.3 88 4-92 128-227 (314)
96 PRK03681 hypA hydrogenase nick 89.0 0.21 4.6E-06 25.8 0.9 11 18-28 70-80 (114)
97 PRK00564 hypA hydrogenase nick 88.9 0.23 4.9E-06 25.8 1.0 11 18-28 71-81 (117)
98 smart00531 TFIIE Transcription 88.6 1.1 2.3E-05 24.2 3.5 37 44-84 97-133 (147)
99 PF13248 zf-ribbon_3: zinc-rib 88.1 0.5 1.1E-05 17.5 1.5 21 3-26 4-24 (26)
100 cd02249 ZZ Zinc finger, ZZ typ 87.6 0.84 1.8E-05 19.4 2.2 21 2-25 1-21 (46)
101 PRK00464 nrdR transcriptional 87.5 0.55 1.2E-05 25.6 1.9 34 2-35 1-45 (154)
102 KOG4173|consensus 87.5 0.19 4.2E-06 28.6 0.2 73 19-94 80-166 (253)
103 COG1571 Predicted DNA-binding 87.4 0.51 1.1E-05 29.9 1.9 30 3-32 352-381 (421)
104 PF01155 HypA: Hydrogenase exp 87.4 0.11 2.3E-06 26.8 -0.8 13 18-30 70-82 (113)
105 PF08274 PhnA_Zn_Ribbon: PhnA 86.8 0.42 9.1E-06 18.5 0.9 22 4-25 5-26 (30)
106 PF01363 FYVE: FYVE zinc finge 86.8 0.51 1.1E-05 21.8 1.4 23 4-27 12-34 (69)
107 KOG3507|consensus 86.8 0.34 7.3E-06 21.8 0.7 9 46-54 37-45 (62)
108 PF07282 OrfB_Zn_ribbon: Putat 86.5 1.9 4.2E-05 19.8 3.3 14 45-58 45-58 (69)
109 PF02892 zf-BED: BED zinc fing 86.4 1.2 2.6E-05 18.6 2.4 21 74-94 16-40 (45)
110 PF09845 DUF2072: Zn-ribbon co 86.4 0.45 9.8E-06 25.2 1.2 26 1-26 1-27 (131)
111 smart00734 ZnF_Rad18 Rad18-lik 85.5 1.1 2.3E-05 16.7 1.8 19 76-95 3-21 (26)
112 PF14446 Prok-RING_1: Prokaryo 85.5 1.1 2.4E-05 20.0 2.0 25 3-28 7-31 (54)
113 PRK05978 hypothetical protein; 85.4 0.82 1.8E-05 24.8 1.9 26 3-28 35-62 (148)
114 COG4332 Uncharacterized protei 85.2 0.65 1.4E-05 26.0 1.5 27 3-29 19-60 (203)
115 KOG1146|consensus 84.9 0.19 4.1E-06 36.0 -0.8 20 77-96 1331-1350(1406)
116 PF14353 CpXC: CpXC protein 84.4 1.1 2.3E-05 23.5 2.0 10 3-12 3-12 (128)
117 PF14634 zf-RING_5: zinc-RING 84.4 1.7 3.6E-05 18.1 2.3 26 3-30 1-26 (44)
118 PF00301 Rubredoxin: Rubredoxi 84.3 0.41 8.9E-06 20.7 0.4 10 2-11 2-11 (47)
119 KOG1280|consensus 84.3 2.3 5E-05 26.4 3.6 37 17-53 78-116 (381)
120 PF02176 zf-TRAF: TRAF-type zi 84.3 1.6 3.6E-05 19.3 2.4 41 45-86 8-54 (60)
121 smart00440 ZnF_C2C2 C2C2 Zinc 83.9 1.7 3.7E-05 17.9 2.2 12 18-29 28-39 (40)
122 PRK14559 putative protein seri 83.9 2.4 5.2E-05 28.7 3.8 25 1-28 1-25 (645)
123 smart00614 ZnF_BED BED zinc fi 83.9 1.1 2.4E-05 19.3 1.7 21 75-95 19-44 (50)
124 COG1773 Rubredoxin [Energy pro 83.8 0.72 1.6E-05 20.6 1.0 12 2-13 4-15 (55)
125 PRK12380 hydrogenase nickel in 83.7 0.57 1.2E-05 24.1 0.8 11 18-28 70-80 (113)
126 COG5151 SSL1 RNA polymerase II 83.5 1.1 2.3E-05 27.5 2.0 24 74-97 388-411 (421)
127 PF05290 Baculo_IE-1: Baculovi 83.4 0.37 8E-06 25.6 0.1 13 17-29 79-91 (140)
128 PF08271 TF_Zn_Ribbon: TFIIB z 83.1 0.87 1.9E-05 19.0 1.2 25 2-26 1-27 (43)
129 TIGR00100 hypA hydrogenase nic 83.1 0.66 1.4E-05 24.0 0.9 12 18-29 70-81 (115)
130 KOG2785|consensus 82.8 1.7 3.6E-05 27.3 2.6 77 19-95 4-89 (390)
131 PRK14714 DNA polymerase II lar 82.7 2.3 4.9E-05 31.0 3.4 21 2-27 668-688 (1337)
132 PF07295 DUF1451: Protein of u 81.8 1.2 2.6E-05 24.2 1.6 8 19-26 113-120 (146)
133 cd02341 ZZ_ZZZ3 Zinc finger, Z 81.6 2.1 4.6E-05 18.5 2.1 22 2-25 1-22 (48)
134 PF01286 XPA_N: XPA protein N- 80.8 1.1 2.3E-05 18.0 0.9 24 3-26 5-29 (34)
135 KOG4167|consensus 80.6 0.38 8.2E-06 32.6 -0.6 25 74-98 792-816 (907)
136 TIGR00686 phnA alkylphosphonat 80.4 1.5 3.2E-05 22.5 1.6 29 3-31 4-32 (109)
137 smart00154 ZnF_AN1 AN1-like Zi 80.4 0.87 1.9E-05 18.7 0.6 11 1-11 12-22 (39)
138 PRK10220 hypothetical protein; 80.0 2.1 4.5E-05 22.0 2.0 29 3-31 5-33 (111)
139 COG3364 Zn-ribbon containing p 79.3 0.68 1.5E-05 23.4 0.2 26 1-26 2-28 (112)
140 COG3091 SprT Zn-dependent meta 78.8 1.5 3.2E-05 23.9 1.3 35 45-84 116-150 (156)
141 cd02337 ZZ_CBP Zinc finger, ZZ 78.6 3 6.6E-05 17.3 2.0 20 2-25 1-20 (41)
142 KOG3408|consensus 78.3 1.9 4E-05 22.6 1.6 26 71-96 54-79 (129)
143 PF05443 ROS_MUCR: ROS/MUCR tr 78.0 2.5 5.4E-05 22.6 2.0 21 74-97 72-92 (132)
144 COG1997 RPL43A Ribosomal prote 77.6 2.9 6.2E-05 20.6 2.0 33 18-60 35-67 (89)
145 cd02335 ZZ_ADA2 Zinc finger, Z 77.2 3.7 8E-05 17.7 2.2 22 2-25 1-22 (49)
146 COG0068 HypF Hydrogenase matur 77.1 0.1 2.2E-06 35.0 -3.9 56 21-83 126-182 (750)
147 KOG2893|consensus 77.1 0.5 1.1E-05 27.7 -0.7 39 48-90 12-50 (341)
148 PF01096 TFIIS_C: Transcriptio 76.7 2 4.4E-05 17.6 1.2 11 18-28 28-38 (39)
149 COG3677 Transposase and inacti 76.6 2.5 5.4E-05 22.4 1.8 15 16-30 51-65 (129)
150 cd00065 FYVE FYVE domain; Zinc 76.4 2.8 6E-05 18.4 1.7 27 3-30 4-30 (57)
151 KOG2807|consensus 76.1 4.6 0.0001 25.0 3.0 22 16-37 288-309 (378)
152 KOG2593|consensus 76.1 5.4 0.00012 25.6 3.3 37 43-82 125-161 (436)
153 TIGR01384 TFS_arch transcripti 75.4 3.2 7E-05 20.8 2.0 26 4-30 3-28 (104)
154 smart00291 ZnF_ZZ Zinc-binding 75.3 4.9 0.00011 16.8 2.3 21 2-25 5-25 (44)
155 PF06397 Desulfoferrod_N: Desu 75.2 0.94 2E-05 18.4 0.0 8 2-9 7-14 (36)
156 PF11023 DUF2614: Protein of u 75.0 1.7 3.6E-05 22.4 0.9 14 48-61 87-100 (114)
157 PF10058 DUF2296: Predicted in 75.0 2 4.4E-05 19.1 1.1 8 46-53 44-51 (54)
158 PF04959 ARS2: Arsenite-resist 74.9 4.3 9.2E-05 23.6 2.6 27 14-40 73-99 (214)
159 PRK00762 hypA hydrogenase nick 74.6 1.6 3.5E-05 22.9 0.8 12 18-30 70-81 (124)
160 COG1198 PriA Primosomal protei 74.5 4 8.7E-05 28.1 2.7 9 46-54 475-483 (730)
161 PF14803 Nudix_N_2: Nudix N-te 74.5 2 4.3E-05 17.1 0.9 23 4-26 3-30 (34)
162 PF13878 zf-C2H2_3: zinc-finge 74.3 2.4 5.2E-05 17.6 1.1 11 3-13 15-25 (41)
163 PF01428 zf-AN1: AN1-like Zinc 73.8 0.65 1.4E-05 19.4 -0.6 11 1-11 13-23 (43)
164 KOG4167|consensus 73.8 0.58 1.3E-05 31.8 -1.1 24 19-42 793-816 (907)
165 PF03811 Zn_Tnp_IS1: InsA N-te 73.7 4.5 9.7E-05 16.4 1.8 9 16-24 27-35 (36)
166 PF00130 C1_1: Phorbol esters/ 73.5 4.9 0.00011 17.3 2.1 24 3-26 13-36 (53)
167 COG4530 Uncharacterized protei 73.4 3 6.4E-05 21.5 1.5 14 43-56 23-36 (129)
168 COG1998 RPS31 Ribosomal protei 73.2 3.6 7.8E-05 18.0 1.6 10 46-55 37-46 (51)
169 KOG2785|consensus 72.0 8.8 0.00019 24.3 3.5 26 18-43 166-191 (390)
170 cd02340 ZZ_NBR1_like Zinc fing 72.0 6 0.00013 16.6 2.1 20 3-25 2-21 (43)
171 PF15269 zf-C2H2_7: Zinc-finge 71.8 4.9 0.00011 17.1 1.8 23 18-40 20-42 (54)
172 cd01121 Sms Sms (bacterial rad 71.6 4.4 9.5E-05 25.5 2.3 24 2-28 1-24 (372)
173 PF12013 DUF3505: Protein of u 71.5 5.2 0.00011 20.3 2.2 24 74-97 80-107 (109)
174 PRK06450 threonine synthase; V 71.0 2.6 5.7E-05 26.0 1.2 25 2-28 4-28 (338)
175 PF00628 PHD: PHD-finger; Int 70.8 6.2 0.00013 16.8 2.1 23 4-28 2-24 (51)
176 TIGR00416 sms DNA repair prote 70.7 3.4 7.4E-05 26.7 1.7 25 2-29 8-32 (454)
177 PRK12722 transcriptional activ 70.6 4 8.6E-05 23.2 1.8 8 4-11 137-144 (187)
178 KOG2593|consensus 70.4 4.8 0.0001 25.9 2.2 37 16-55 126-162 (436)
179 PRK11823 DNA repair protein Ra 70.1 3.6 7.7E-05 26.5 1.7 24 2-28 8-31 (446)
180 PF09082 DUF1922: Domain of un 70.0 1.2 2.6E-05 20.8 -0.3 26 2-29 4-30 (68)
181 smart00064 FYVE Protein presen 69.9 4.5 9.8E-05 18.5 1.7 10 20-29 12-21 (68)
182 PF13453 zf-TFIIB: Transcripti 69.7 5.2 0.00011 16.4 1.7 19 74-92 19-37 (41)
183 PF13445 zf-RING_UBOX: RING-ty 69.6 7.7 0.00017 16.3 2.2 28 4-33 1-28 (43)
184 PF04641 Rtf2: Rtf2 RING-finge 68.8 5.4 0.00012 23.7 2.2 50 1-58 113-162 (260)
185 PF00569 ZZ: Zinc finger, ZZ t 68.6 4.1 9E-05 17.2 1.3 22 2-25 5-26 (46)
186 PF09297 zf-NADH-PPase: NADH p 68.4 3.4 7.4E-05 15.9 0.9 23 4-26 6-29 (32)
187 cd00029 C1 Protein kinase C co 68.4 4.7 0.0001 16.9 1.5 7 47-53 29-35 (50)
188 PRK00420 hypothetical protein; 68.3 6.6 0.00014 20.4 2.2 25 3-29 25-51 (112)
189 PF11789 zf-Nse: Zinc-finger o 67.8 9.9 0.00021 17.0 2.5 31 45-79 23-53 (57)
190 PRK12496 hypothetical protein; 67.6 5 0.00011 22.2 1.8 12 18-29 127-138 (164)
191 TIGR03826 YvyF flagellar opero 67.2 1.5 3.3E-05 23.5 -0.2 23 3-27 5-27 (137)
192 PTZ00255 60S ribosomal protein 66.4 4.4 9.5E-05 20.1 1.2 33 18-60 36-68 (90)
193 PF14206 Cys_rich_CPCC: Cystei 65.8 6.9 0.00015 18.9 1.8 24 2-25 2-27 (78)
194 PF11781 RRN7: RNA polymerase 65.7 5.5 0.00012 16.0 1.3 22 4-25 11-32 (36)
195 PRK06260 threonine synthase; V 65.6 4.2 9.2E-05 25.7 1.4 26 2-28 4-29 (397)
196 PF08209 Sgf11: Sgf11 (transcr 65.5 6 0.00013 15.7 1.4 11 75-85 5-15 (33)
197 cd00974 DSRD Desulforedoxin (D 65.3 2.7 5.8E-05 16.5 0.3 9 2-10 5-13 (34)
198 PRK11032 hypothetical protein; 65.3 5.1 0.00011 22.1 1.5 8 19-26 125-132 (160)
199 KOG2907|consensus 65.2 4.3 9.3E-05 21.0 1.1 38 47-85 75-113 (116)
200 TIGR00570 cdk7 CDK-activating 65.2 19 0.00041 22.3 3.9 53 2-59 4-56 (309)
201 PF08792 A2L_zn_ribbon: A2L zi 64.5 5.8 0.00012 15.7 1.2 11 18-28 21-31 (33)
202 PRK12860 transcriptional activ 64.5 5.8 0.00013 22.6 1.6 8 46-53 154-161 (189)
203 PF05766 NinG: Bacteriophage L 64.1 6.8 0.00015 22.3 1.9 26 1-26 6-32 (189)
204 smart00109 C1 Protein kinase C 64.1 7.8 0.00017 16.0 1.8 8 4-11 14-21 (49)
205 PRK07591 threonine synthase; V 64.0 4.8 0.0001 25.7 1.4 25 2-28 19-43 (421)
206 PF04810 zf-Sec23_Sec24: Sec23 63.8 7.5 0.00016 15.9 1.6 24 3-26 4-32 (40)
207 TIGR00319 desulf_FeS4 desulfof 63.6 2.9 6.2E-05 16.4 0.3 9 2-10 8-16 (34)
208 PRK08329 threonine synthase; V 63.5 7.9 0.00017 24.0 2.2 25 1-28 1-25 (347)
209 PHA02942 putative transposase; 63.3 20 0.00043 22.8 3.9 13 46-58 342-354 (383)
210 PF13451 zf-trcl: Probable zin 63.1 3.9 8.6E-05 17.8 0.7 16 72-87 2-17 (49)
211 KOG2906|consensus 63.0 0.25 5.4E-06 24.7 -3.4 30 2-31 2-34 (105)
212 PF15135 UPF0515: Uncharacteri 62.4 9.8 0.00021 22.7 2.3 11 75-85 156-166 (278)
213 PF11672 DUF3268: Protein of u 62.3 5.7 0.00012 20.2 1.3 7 75-81 32-38 (102)
214 PF04606 Ogr_Delta: Ogr/Delta- 62.3 4.6 9.9E-05 17.2 0.8 6 4-9 2-7 (47)
215 PF13005 zf-IS66: zinc-finger 61.9 7.4 0.00016 16.3 1.4 10 3-12 4-13 (47)
216 PHA02998 RNA polymerase subuni 61.3 1.9 4.1E-05 24.2 -0.6 42 46-87 143-184 (195)
217 smart00504 Ubox Modified RING 60.2 15 0.00032 16.2 3.5 45 2-57 2-46 (63)
218 PF07975 C1_4: TFIIH C1-like d 58.4 2.8 6E-05 18.5 -0.2 17 45-61 20-36 (51)
219 PF05495 zf-CHY: CHY zinc fing 58.4 3.6 7.8E-05 19.3 0.2 31 46-84 41-71 (71)
220 PF13824 zf-Mss51: Zinc-finger 57.5 6.6 0.00014 17.6 0.9 7 2-8 15-21 (55)
221 PF08790 zf-LYAR: LYAR-type C2 57.3 3.2 7E-05 15.8 -0.1 9 48-56 2-10 (28)
222 KOG2231|consensus 57.1 30 0.00065 23.9 4.1 45 20-68 184-234 (669)
223 COG5216 Uncharacterized conser 57.1 8.8 0.00019 17.4 1.2 32 18-55 22-53 (67)
224 COG4847 Uncharacterized protei 56.9 2.3 5E-05 21.2 -0.6 21 2-22 7-35 (103)
225 KOG2482|consensus 56.8 7.3 0.00016 24.4 1.3 23 74-96 195-217 (423)
226 TIGR00280 L37a ribosomal prote 56.7 6.6 0.00014 19.6 0.9 33 18-60 35-67 (91)
227 PLN02294 cytochrome c oxidase 56.5 7.7 0.00017 21.7 1.2 19 67-86 135-153 (174)
228 COG5349 Uncharacterized protei 56.4 6.2 0.00013 20.8 0.8 26 3-28 23-50 (126)
229 COG1066 Sms Predicted ATP-depe 56.4 7.7 0.00017 25.1 1.3 23 2-27 8-30 (456)
230 PRK04351 hypothetical protein; 56.3 8.7 0.00019 21.0 1.4 34 17-58 111-144 (149)
231 PF05129 Elf1: Transcription e 55.9 4.7 0.0001 19.5 0.3 14 46-59 46-59 (81)
232 PRK12286 rpmF 50S ribosomal pr 55.1 13 0.00029 16.7 1.7 8 19-26 28-35 (57)
233 PF03563 Bunya_G2: Bunyavirus 55.0 19 0.0004 21.8 2.6 16 23-38 255-270 (285)
234 COG5152 Uncharacterized conser 54.5 5 0.00011 23.0 0.3 17 14-30 192-208 (259)
235 PF15616 TerY-C: TerY-C metal 54.5 8.7 0.00019 20.5 1.2 13 15-27 102-114 (131)
236 TIGR01031 rpmF_bact ribosomal 54.3 13 0.00028 16.6 1.5 8 19-26 27-34 (55)
237 PF02891 zf-MIZ: MIZ/SP-RING z 54.2 5.5 0.00012 17.3 0.4 8 75-82 42-49 (50)
238 TIGR03844 cysteate_syn cysteat 53.3 8.8 0.00019 24.4 1.3 22 2-25 3-24 (398)
239 COG1675 TFA1 Transcription ini 52.9 32 0.00069 19.5 3.2 33 43-84 110-142 (176)
240 PF03119 DNA_ligase_ZBD: NAD-d 52.3 8.2 0.00018 14.5 0.7 18 4-21 2-20 (28)
241 PRK00418 DNA gyrase inhibitor; 52.3 13 0.00028 17.1 1.4 9 3-11 8-16 (62)
242 PF14311 DUF4379: Domain of un 51.3 18 0.00039 15.8 1.8 13 47-59 29-41 (55)
243 COG0675 Transposase and inacti 50.2 26 0.00057 21.2 3.0 15 45-59 321-335 (364)
244 cd00924 Cyt_c_Oxidase_Vb Cytoc 49.8 11 0.00023 19.1 1.0 19 67-86 73-91 (97)
245 PRK14704 anaerobic ribonucleos 49.8 13 0.00029 25.2 1.7 19 4-26 562-580 (618)
246 TIGR02443 conserved hypothetic 49.7 15 0.00033 16.7 1.4 26 3-28 11-41 (59)
247 PF04423 Rad50_zn_hook: Rad50 49.6 7.5 0.00016 17.0 0.4 13 48-60 22-34 (54)
248 PF06750 DiS_P_DiS: Bacterial 49.5 33 0.00073 17.0 2.9 12 19-30 34-45 (92)
249 cd02336 ZZ_RSC8 Zinc finger, Z 49.4 9.5 0.00021 16.2 0.7 11 2-12 1-11 (45)
250 smart00249 PHD PHD zinc finger 48.8 20 0.00044 14.3 2.2 23 4-28 2-24 (47)
251 PRK03976 rpl37ae 50S ribosomal 48.7 10 0.00022 18.9 0.8 33 18-60 36-68 (90)
252 TIGR00595 priA primosomal prot 48.7 24 0.00052 23.4 2.7 7 19-25 241-247 (505)
253 COG1594 RPB9 DNA-directed RNA 48.6 5.9 0.00013 20.5 0.0 28 4-31 5-35 (113)
254 COG2331 Uncharacterized protei 48.1 4.8 0.0001 19.3 -0.3 32 17-55 11-42 (82)
255 COG3024 Uncharacterized protei 47.9 10 0.00022 17.5 0.7 10 3-12 9-18 (65)
256 PF06827 zf-FPG_IleRS: Zinc fi 47.7 12 0.00026 14.1 0.8 23 3-25 3-28 (30)
257 KOG0717|consensus 47.5 14 0.00031 24.2 1.5 21 75-95 293-313 (508)
258 PRK08197 threonine synthase; V 47.4 14 0.0003 23.5 1.5 24 2-27 8-31 (394)
259 PF10013 DUF2256: Uncharacteri 47.3 15 0.00033 15.5 1.1 12 76-87 10-21 (42)
260 cd01675 RNR_III Class III ribo 47.0 16 0.00036 24.4 1.8 7 47-53 533-539 (555)
261 PF04780 DUF629: Protein of un 46.7 20 0.00043 23.6 2.1 21 75-95 58-78 (466)
262 PRK12495 hypothetical protein; 46.7 18 0.00039 21.2 1.7 25 2-28 43-68 (226)
263 PRK14892 putative transcriptio 46.6 22 0.00048 18.0 1.9 34 18-58 21-54 (99)
264 PRK05452 anaerobic nitric oxid 46.5 11 0.00025 24.6 1.0 16 15-30 422-437 (479)
265 KOG2071|consensus 46.4 15 0.00033 24.7 1.6 26 72-97 416-441 (579)
266 cd02339 ZZ_Mind_bomb Zinc fing 46.1 26 0.00057 14.8 2.1 20 4-25 3-22 (45)
267 TIGR00143 hypF [NiFe] hydrogen 46.0 0.34 7.4E-06 32.8 -5.8 59 18-83 89-149 (711)
268 PF10263 SprT-like: SprT-like 45.7 15 0.00032 19.8 1.3 32 46-85 123-154 (157)
269 PHA03082 DNA-dependent RNA pol 45.7 7.7 0.00017 17.5 0.2 8 21-28 7-14 (63)
270 TIGR02827 RNR_anaer_Bdell anae 45.5 16 0.00034 24.8 1.6 7 19-25 547-553 (586)
271 PF11931 DUF3449: Domain of un 45.0 7.1 0.00015 22.4 0.0 7 2-8 102-108 (196)
272 PF13901 DUF4206: Domain of un 44.8 29 0.00064 19.9 2.4 27 2-28 153-182 (202)
273 PF10276 zf-CHCC: Zinc-finger 44.6 10 0.00022 15.8 0.4 11 74-84 29-39 (40)
274 KOG3002|consensus 44.3 47 0.001 20.6 3.3 76 16-95 78-160 (299)
275 PF05864 Chordopox_RPO7: Chord 43.9 8.3 0.00018 17.4 0.1 8 21-28 7-14 (63)
276 PF09526 DUF2387: Probable met 43.7 19 0.00041 17.0 1.3 28 3-30 10-42 (71)
277 PRK07111 anaerobic ribonucleos 43.5 18 0.0004 25.2 1.7 8 19-26 694-701 (735)
278 PRK05638 threonine synthase; V 43.4 20 0.00042 23.2 1.7 24 2-28 2-25 (442)
279 COG1545 Predicted nucleic-acid 42.2 19 0.00041 19.4 1.3 10 4-13 32-41 (140)
280 COG4306 Uncharacterized protei 42.2 28 0.00061 18.5 1.9 12 18-29 68-79 (160)
281 COG1326 Uncharacterized archae 41.9 47 0.001 19.2 2.8 11 46-56 30-40 (201)
282 TIGR02487 NrdD anaerobic ribon 41.9 22 0.00049 24.0 1.8 8 19-26 539-546 (579)
283 PF11228 DUF3027: Protein of u 41.8 20 0.00044 20.5 1.4 27 2-28 146-172 (193)
284 PRK05580 primosome assembly pr 41.5 34 0.00075 23.6 2.7 6 48-53 423-428 (679)
285 COG4888 Uncharacterized Zn rib 41.3 19 0.0004 18.4 1.1 40 15-58 19-58 (104)
286 PRK08579 anaerobic ribonucleos 40.8 22 0.00049 24.3 1.7 8 19-26 583-590 (625)
287 PF14569 zf-UDP: Zinc-binding 40.2 27 0.00059 16.9 1.5 50 3-57 11-62 (80)
288 PF09943 DUF2175: Uncharacteri 40.0 5.6 0.00012 20.2 -0.8 20 2-21 3-30 (101)
289 TIGR02159 PA_CoA_Oxy4 phenylac 39.8 13 0.00029 20.2 0.5 11 47-57 131-141 (146)
290 PTZ00448 hypothetical protein; 39.4 27 0.00059 22.2 1.8 23 74-96 314-336 (373)
291 PF02150 RNA_POL_M_15KD: RNA p 39.4 6.8 0.00015 15.6 -0.5 24 4-27 4-29 (35)
292 COG2824 PhnA Uncharacterized Z 39.1 24 0.00052 18.2 1.3 27 3-29 5-31 (112)
293 COG0375 HybF Zn finger protein 38.9 16 0.00034 19.1 0.7 11 18-28 70-80 (115)
294 KOG3362|consensus 38.5 12 0.00027 20.3 0.3 20 47-66 130-149 (156)
295 PF00641 zf-RanBP: Zn-finger i 38.5 11 0.00024 14.2 0.1 7 3-9 6-12 (30)
296 PF05741 zf-nanos: Nanos RNA b 38.4 14 0.0003 16.6 0.4 9 2-10 34-42 (55)
297 PF10083 DUF2321: Uncharacteri 37.9 30 0.00066 19.2 1.7 15 45-59 67-81 (158)
298 PF06906 DUF1272: Protein of u 37.9 43 0.00094 15.1 1.9 22 4-25 8-33 (57)
299 PF01215 COX5B: Cytochrome c o 37.9 16 0.00035 19.7 0.7 18 68-86 107-124 (136)
300 PF07191 zinc-ribbons_6: zinc- 37.8 14 0.0003 17.5 0.3 25 3-28 3-27 (70)
301 TIGR03831 YgiT_finger YgiT-typ 37.6 15 0.00032 15.0 0.4 11 75-85 33-43 (46)
302 COG5112 UFD2 U1-like Zn-finger 37.4 23 0.00051 18.2 1.1 22 74-95 55-76 (126)
303 COG4957 Predicted transcriptio 37.0 26 0.00056 19.0 1.3 23 47-72 77-99 (148)
304 PRK11088 rrmA 23S rRNA methylt 37.0 40 0.00087 20.1 2.3 25 2-28 3-27 (272)
305 TIGR01053 LSD1 zinc finger dom 36.9 33 0.00071 13.3 2.1 22 4-25 4-26 (31)
306 PF14787 zf-CCHC_5: GAG-polypr 36.9 9.6 0.00021 15.4 -0.2 13 76-88 4-16 (36)
307 PF01927 Mut7-C: Mut7-C RNAse 36.7 37 0.0008 18.3 1.9 46 19-64 92-142 (147)
308 PF14369 zf-RING_3: zinc-finge 36.4 18 0.00038 14.4 0.5 10 76-85 23-32 (35)
309 PF10080 DUF2318: Predicted me 36.2 21 0.00046 18.2 0.9 25 4-29 38-63 (102)
310 cd02345 ZZ_dah Zinc finger, ZZ 36.1 33 0.00071 14.8 1.4 21 3-25 2-22 (49)
311 PF02318 FYVE_2: FYVE-type zin 36.0 36 0.00078 17.6 1.7 10 72-81 92-101 (118)
312 CHL00174 accD acetyl-CoA carbo 36.0 23 0.00051 21.8 1.2 11 47-57 58-68 (296)
313 PF01780 Ribosomal_L37ae: Ribo 36.0 18 0.00039 18.0 0.6 31 45-85 34-64 (90)
314 KOG2923|consensus 35.9 29 0.00062 16.1 1.2 33 18-56 22-54 (67)
315 PF05191 ADK_lid: Adenylate ki 35.9 9.7 0.00021 15.3 -0.3 9 3-11 3-11 (36)
316 PF13639 zf-RING_2: Ring finge 35.6 39 0.00084 13.7 2.1 25 4-30 3-27 (44)
317 PF05280 FlhC: Flagellar trans 35.5 18 0.00038 20.4 0.6 8 4-11 137-144 (175)
318 PTZ00043 cytochrome c oxidase 34.9 23 0.00051 20.9 1.0 15 72-86 179-193 (268)
319 PF02591 DUF164: Putative zinc 34.5 48 0.001 14.5 2.3 13 70-82 42-54 (56)
320 cd02338 ZZ_PCMF_like Zinc fing 34.3 35 0.00077 14.6 1.3 21 3-25 2-22 (49)
321 smart00132 LIM Zinc-binding do 34.1 25 0.00054 13.4 0.8 8 2-9 28-35 (39)
322 COG1779 C4-type Zn-finger prot 34.1 23 0.00049 20.5 0.9 11 19-29 44-54 (201)
323 PF00412 LIM: LIM domain; Int 34.1 33 0.00071 14.7 1.3 12 2-13 27-38 (58)
324 PF13696 zf-CCHC_2: Zinc knuck 34.0 17 0.00037 14.3 0.3 8 2-9 9-16 (32)
325 PLN02569 threonine synthase 33.8 33 0.0007 22.7 1.6 25 2-28 50-74 (484)
326 PF04438 zf-HIT: HIT zinc fing 33.6 26 0.00057 13.4 0.8 11 74-84 13-23 (30)
327 cd04476 RPA1_DBD_C RPA1_DBD_C: 33.6 37 0.0008 18.6 1.6 10 18-27 51-60 (166)
328 TIGR00627 tfb4 transcription f 33.5 40 0.00087 20.6 1.9 8 75-82 256-263 (279)
329 cd02334 ZZ_dystrophin Zinc fin 33.4 49 0.0011 14.3 1.8 21 3-25 2-22 (49)
330 PF14319 Zn_Tnp_IS91: Transpos 33.0 27 0.00058 18.0 1.0 13 15-27 39-51 (111)
331 PF06170 DUF983: Protein of un 33.0 29 0.00062 17.1 1.0 11 3-13 10-20 (86)
332 PRK05654 acetyl-CoA carboxylas 32.8 26 0.00056 21.5 1.0 12 47-58 47-58 (292)
333 smart00647 IBR In Between Ring 32.5 40 0.00086 14.8 1.4 15 44-58 38-52 (64)
334 PLN03238 probable histone acet 32.4 68 0.0015 19.8 2.6 23 45-67 47-69 (290)
335 PLN02638 cellulose synthase A 31.8 72 0.0016 23.7 3.0 50 3-57 19-70 (1079)
336 PF09965 DUF2199: Uncharacteri 31.7 26 0.00057 19.2 0.8 11 2-12 1-11 (148)
337 COG1867 TRM1 N2,N2-dimethylgua 31.6 31 0.00066 22.1 1.2 26 2-27 241-266 (380)
338 PF01485 IBR: IBR domain; Int 31.4 40 0.00087 14.7 1.4 11 47-57 41-51 (64)
339 TIGR00515 accD acetyl-CoA carb 31.3 14 0.0003 22.5 -0.2 11 47-57 46-56 (285)
340 PF09332 Mcm10: Mcm10 replicat 31.2 18 0.00038 22.8 0.2 12 18-29 285-296 (344)
341 smart00731 SprT SprT homologue 30.4 40 0.00086 18.1 1.4 32 46-84 112-143 (146)
342 PLN03208 E3 ubiquitin-protein 30.2 1.2E+02 0.0025 17.6 3.5 13 46-58 68-80 (193)
343 COG1503 eRF1 Peptide chain rel 30.2 29 0.00064 22.4 1.0 10 2-11 328-337 (411)
344 TIGR00244 transcriptional regu 30.2 49 0.0011 18.2 1.7 17 18-34 28-44 (147)
345 PRK08271 anaerobic ribonucleos 30.1 44 0.00096 23.0 1.8 8 19-26 581-588 (623)
346 COG1327 Predicted transcriptio 30.0 44 0.00096 18.5 1.5 17 17-33 27-43 (156)
347 PLN02748 tRNA dimethylallyltra 29.9 47 0.001 22.0 1.9 24 73-96 417-441 (468)
348 PF12647 RNHCP: RNHCP domain; 29.5 52 0.0011 16.5 1.6 25 1-25 4-31 (92)
349 PF09855 DUF2082: Nucleic-acid 29.0 24 0.00052 16.3 0.4 7 75-81 1-7 (64)
350 PLN02436 cellulose synthase A 28.8 88 0.0019 23.3 3.0 50 3-57 38-89 (1094)
351 PF14690 zf-ISL3: zinc-finger 28.6 33 0.00072 14.1 0.8 9 1-9 2-10 (47)
352 COG4391 Uncharacterized protei 28.4 43 0.00093 15.4 1.1 41 14-58 20-60 (62)
353 PF12172 DUF35_N: Rubredoxin-l 28.3 28 0.0006 13.7 0.5 7 4-10 14-20 (37)
354 PRK03988 translation initiatio 28.3 35 0.00075 18.5 1.0 7 48-54 125-131 (138)
355 PRK04338 N(2),N(2)-dimethylgua 28.2 38 0.00082 21.6 1.2 26 2-27 245-270 (382)
356 TIGR00311 aIF-2beta translatio 28.2 34 0.00073 18.4 0.9 7 48-54 120-126 (133)
357 PF13821 DUF4187: Domain of un 28.2 33 0.00071 15.3 0.7 16 75-90 28-43 (55)
358 PF05876 Terminase_GpA: Phage 28.1 69 0.0015 21.7 2.4 28 3-30 202-241 (557)
359 KOG1842|consensus 27.8 35 0.00076 22.4 1.0 22 74-95 15-36 (505)
360 KOG0978|consensus 27.6 16 0.00036 25.2 -0.4 19 73-91 677-695 (698)
361 KOG2817|consensus 27.6 62 0.0013 20.9 2.0 16 67-82 367-382 (394)
362 PRK01343 zinc-binding protein; 27.1 41 0.00088 15.2 0.9 10 3-12 11-20 (57)
363 smart00709 Zpr1 Duplicated dom 27.1 43 0.00093 18.6 1.2 11 18-28 29-39 (160)
364 KOG1994|consensus 27.1 39 0.00085 20.1 1.0 21 73-93 238-258 (268)
365 COG4338 Uncharacterized protei 27.0 29 0.00064 15.1 0.4 12 76-87 14-25 (54)
366 PRK00415 rps27e 30S ribosomal 26.9 65 0.0014 14.7 1.5 13 46-58 30-42 (59)
367 cd02344 ZZ_HERC2 Zinc finger, 26.8 66 0.0014 13.7 2.1 20 4-25 3-22 (45)
368 COG2816 NPY1 NTP pyrophosphohy 26.8 67 0.0014 19.8 2.0 24 4-27 114-138 (279)
369 PF08646 Rep_fac-A_C: Replicat 26.6 31 0.00068 18.4 0.6 22 6-27 25-46 (146)
370 PLN02915 cellulose synthase A 26.6 1E+02 0.0022 22.9 3.0 50 3-57 17-68 (1044)
371 TIGR03830 CxxCG_CxxCG_HTH puta 26.5 89 0.0019 16.0 2.3 13 75-87 32-44 (127)
372 TIGR03829 YokU_near_AblA uncha 26.5 77 0.0017 15.8 1.9 16 75-90 36-51 (89)
373 COG5236 Uncharacterized conser 26.5 85 0.0018 20.1 2.4 72 19-95 221-302 (493)
374 KOG3183|consensus 26.4 27 0.00059 20.8 0.4 11 1-11 23-33 (250)
375 KOG3277|consensus 26.3 47 0.001 18.4 1.2 36 16-54 77-112 (165)
376 PF14255 Cys_rich_CPXG: Cystei 25.9 31 0.00068 15.2 0.4 9 76-84 2-10 (52)
377 PF03884 DUF329: Domain of unk 25.7 33 0.00073 15.5 0.5 11 3-13 4-14 (57)
378 smart00396 ZnF_UBR1 Putative z 25.6 86 0.0019 14.7 1.9 20 6-26 2-21 (71)
379 PLN02189 cellulose synthase 25.2 1.1E+02 0.0025 22.7 3.0 50 3-57 36-87 (1040)
380 PF09963 DUF2197: Uncharacteri 25.0 78 0.0017 14.3 1.6 7 47-53 32-38 (56)
381 KOG2846|consensus 24.9 48 0.0011 20.8 1.2 22 6-27 222-251 (328)
382 PF14375 Cys_rich_CWC: Cystein 24.8 49 0.0011 14.2 1.0 11 4-14 1-11 (50)
383 PRK02935 hypothetical protein; 24.7 48 0.001 17.1 1.0 14 47-60 87-100 (110)
384 KOG2636|consensus 24.6 66 0.0014 21.3 1.8 27 67-93 394-421 (497)
385 COG2093 DNA-directed RNA polym 24.5 61 0.0013 15.0 1.2 6 21-26 21-26 (64)
386 KOG1729|consensus 24.5 6.7 0.00015 23.9 -2.3 7 20-26 170-176 (288)
387 COG1096 Predicted RNA-binding 24.5 58 0.0013 18.7 1.4 10 18-27 165-174 (188)
388 COG5319 Uncharacterized protei 24.3 87 0.0019 16.9 1.9 24 27-54 17-40 (142)
389 KOG4317|consensus 24.2 18 0.00038 22.6 -0.6 10 19-28 20-29 (383)
390 PF06676 DUF1178: Protein of u 24.1 1.1E+02 0.0025 16.8 2.4 26 27-56 17-42 (148)
391 COG4640 Predicted membrane pro 24.0 87 0.0019 20.5 2.2 30 4-36 4-33 (465)
392 PF10164 DUF2367: Uncharacteri 23.5 42 0.00092 17.0 0.7 13 72-84 86-98 (98)
393 smart00290 ZnF_UBP Ubiquitin C 23.2 77 0.0017 13.2 1.9 11 18-28 11-21 (50)
394 PRK09263 anaerobic ribonucleos 23.2 82 0.0018 22.2 2.1 8 19-26 660-667 (711)
395 KOG0696|consensus 23.1 21 0.00045 23.5 -0.5 46 35-81 82-128 (683)
396 PF04161 Arv1: Arv1-like famil 23.1 53 0.0012 19.0 1.1 26 2-27 1-33 (208)
397 PF01258 zf-dskA_traR: Prokary 23.0 43 0.00094 13.1 0.6 6 4-9 6-11 (36)
398 PF09862 DUF2089: Protein of u 23.0 57 0.0012 17.1 1.1 19 4-25 1-19 (113)
399 PF14445 Prok-RING_2: Prokaryo 22.9 7.6 0.00016 17.0 -1.7 12 18-29 7-18 (57)
400 KOG0782|consensus 22.9 17 0.00036 24.8 -1.0 50 33-88 240-290 (1004)
401 PF14205 Cys_rich_KTR: Cystein 22.8 26 0.00056 15.7 -0.1 8 74-81 28-35 (55)
402 KOG2703|consensus 22.6 34 0.00074 22.1 0.3 10 1-10 68-77 (460)
403 PF02146 SIR2: Sir2 family; I 22.6 1.2E+02 0.0025 16.9 2.4 12 47-58 106-117 (178)
404 PF04981 NMD3: NMD3 family ; 22.5 40 0.00087 19.8 0.6 12 47-58 36-47 (236)
405 PRK00241 nudC NADH pyrophospha 22.4 78 0.0017 19.0 1.7 24 4-27 102-126 (256)
406 COG1439 Predicted nucleic acid 22.3 39 0.00085 19.2 0.5 13 17-29 138-150 (177)
407 PTZ00303 phosphatidylinositol 22.3 74 0.0016 23.0 1.8 26 4-29 463-492 (1374)
408 PF13597 NRDD: Anaerobic ribon 22.2 42 0.00092 22.6 0.7 8 47-54 505-512 (546)
409 TIGR00320 dfx_rbo desulfoferro 22.0 37 0.0008 18.0 0.3 10 2-11 8-17 (125)
410 COG4896 Uncharacterized protei 21.8 59 0.0013 15.0 0.9 9 46-54 31-39 (68)
411 PRK12775 putative trifunctiona 21.7 48 0.001 24.2 0.9 9 18-26 821-829 (1006)
412 CHL00112 rpl28 ribosomal prote 21.5 41 0.00088 15.5 0.4 8 3-10 4-11 (63)
413 PF12907 zf-met2: Zinc-binding 21.4 62 0.0013 13.5 0.9 20 75-94 2-24 (40)
414 PRK12336 translation initiatio 21.4 53 0.0011 19.0 0.9 11 18-28 119-129 (201)
415 PF03691 UPF0167: Uncharacteri 21.3 53 0.0011 18.7 0.8 22 3-24 26-55 (176)
416 PLN02195 cellulose synthase A 21.0 1.6E+02 0.0034 21.9 3.1 50 3-57 8-59 (977)
417 PLN03239 histone acetyltransfe 20.9 91 0.002 19.9 1.8 24 72-95 104-127 (351)
418 PRK14873 primosome assembly pr 20.9 72 0.0016 22.2 1.5 9 46-54 422-430 (665)
419 KOG4727|consensus 20.5 76 0.0016 18.0 1.3 21 74-94 75-95 (193)
420 PF13842 Tnp_zf-ribbon_2: DDE_ 20.2 79 0.0017 12.2 1.5 8 18-25 16-23 (32)
421 smart00401 ZnF_GATA zinc finge 20.2 1E+02 0.0022 13.4 2.0 10 2-11 4-13 (52)
No 1
>KOG2462|consensus
Probab=99.96 E-value=2.4e-29 Score=140.83 Aligned_cols=94 Identities=30% Similarity=0.657 Sum_probs=65.3
Q ss_pred CCCCCCCCccCCCC--------------CCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccchhHHHHHH
Q psy3500 2 YHCKTCSTLSRPNI--------------SYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHER 67 (98)
Q Consensus 2 ~~c~~c~~~~~~~~--------------~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~ 67 (98)
|+|++||+.+.... .+.+.|..|++.|.....|.+|+++|. .+++|++||+.|.+...|+.|++
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiR 208 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIR 208 (279)
T ss_pred eeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccc
Confidence 66777776544322 345667777777777777777777666 45677777777777777777777
Q ss_pred hhCCCCCeecCcCcccccChHHHHHHHhhh
Q psy3500 68 KHTGDKPYICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 68 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
+||||+||.|+.|+++|...++|+.|+++|
T Consensus 209 THTGEKPF~C~hC~kAFADRSNLRAHmQTH 238 (279)
T KOG2462|consen 209 THTGEKPFSCPHCGKAFADRSNLRAHMQTH 238 (279)
T ss_pred cccCCCCccCCcccchhcchHHHHHHHHhh
Confidence 777777777777777777777777777776
No 2
>KOG2462|consensus
Probab=99.95 E-value=4.4e-28 Score=135.79 Aligned_cols=95 Identities=25% Similarity=0.528 Sum_probs=88.6
Q ss_pred CCCCCCCCCccC---------CCCCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccchhHHHHHHhhCC
Q psy3500 1 MYHCKTCSTLSR---------PNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHTG 71 (98)
Q Consensus 1 ~~~c~~c~~~~~---------~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~ 71 (98)
.|.|++||+.++ .++.++++|.+||+.|...=.|+.|+++|+||+||.|+.|++.|..+++|+.|+++|.+
T Consensus 161 a~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~ 240 (279)
T KOG2462|consen 161 AFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSD 240 (279)
T ss_pred cccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcC
Confidence 378999999775 34457899999999999999999999999999999999999999999999999999999
Q ss_pred CCCeecCcCcccccChHHHHHHHh
Q psy3500 72 DKPYICQQCRDTFSSLYLFRNHLQ 95 (98)
Q Consensus 72 ~~~~~C~~C~~~f~~~~~l~~H~~ 95 (98)
.++|+|..|++.|...+-|..|..
T Consensus 241 ~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 241 VKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred CccccCcchhhHHHHHHHHHHhhh
Confidence 999999999999999999999974
No 3
>KOG3576|consensus
Probab=99.68 E-value=6.4e-18 Score=91.97 Aligned_cols=79 Identities=28% Similarity=0.627 Sum_probs=66.1
Q ss_pred CceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccchhHHHHHHhhCCCCCeecCcCcccccChHHHHHHHh
Q psy3500 17 YKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNHLQ 95 (98)
Q Consensus 17 ~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 95 (98)
-.+.|.+|++.|..-..|.+|++.|..-+.+.|..||++|...-.|.+|.++|+|.+||+|..|+++|.+.-.|..|++
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHH
Confidence 4588888888888888888888888877778888888888888888888888888888888888888888888888864
No 4
>KOG3576|consensus
Probab=99.68 E-value=1.4e-17 Score=90.68 Aligned_cols=96 Identities=30% Similarity=0.564 Sum_probs=83.2
Q ss_pred CCCCCCCCccC-----------CCCCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccchhHHHHHHhhC
Q psy3500 2 YHCKTCSTLSR-----------PNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHT 70 (98)
Q Consensus 2 ~~c~~c~~~~~-----------~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~ 70 (98)
|.|.+||+.|. ++.-+.+.|..||+.|...-.|++|+++|++-+||.|..|++.|...-.|..|.+.-.
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvh 197 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVH 197 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHc
Confidence 78999999775 5566789999999999999999999999999999999999999999999999976322
Q ss_pred -----------CCCCeecCcCcccccChHHHHHHHhhh
Q psy3500 71 -----------GDKPYICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 71 -----------~~~~~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
.++-|.|..||.+-.....+..|++.|
T Consensus 198 gv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~ 235 (267)
T KOG3576|consen 198 GVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLH 235 (267)
T ss_pred CchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhc
Confidence 246789999999888888888887765
No 5
>KOG3623|consensus
Probab=99.67 E-value=1.4e-17 Score=104.14 Aligned_cols=79 Identities=29% Similarity=0.692 Sum_probs=75.2
Q ss_pred CCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccchhHHHHHHhhCCCCCeecCcCcccccChHHHHHHH
Q psy3500 16 SYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNHL 94 (98)
Q Consensus 16 ~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 94 (98)
+-.|.|..|++.|...+.|.+|.--|+|.+||.|.+|.+.|...-.|..|.+.|.|++||.|.+|++.|.+......||
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 3469999999999999999999999999999999999999999999999999999999999999999999998888886
No 6
>KOG1074|consensus
Probab=99.61 E-value=6.1e-17 Score=102.31 Aligned_cols=80 Identities=28% Similarity=0.608 Sum_probs=63.0
Q ss_pred ceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccchhHHHHHHhhCCC----CCeecC---cCcccccChHHH
Q psy3500 18 KYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHTGD----KPYICQ---QCRDTFSSLYLF 90 (98)
Q Consensus 18 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~----~~~~C~---~C~~~f~~~~~l 90 (98)
+-.|..|.+...-.+.|+.|.++|++++||.|.+|++.|....+|+.|+..|... ..+.|+ .|-+.|...-.|
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~l 684 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTL 684 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccc
Confidence 4678888888888888888888888888888888888888888888888776543 246677 777888888888
Q ss_pred HHHHhhh
Q psy3500 91 RNHLQSH 97 (98)
Q Consensus 91 ~~H~~~h 97 (98)
..|+++|
T Consensus 685 pQhIriH 691 (958)
T KOG1074|consen 685 PQHIRIH 691 (958)
T ss_pred cceEEee
Confidence 8887776
No 7
>KOG3608|consensus
Probab=99.58 E-value=5.2e-16 Score=90.58 Aligned_cols=92 Identities=29% Similarity=0.646 Sum_probs=78.0
Q ss_pred CCCCCCccCCCC-------------CCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccchhHHHHHHh-h
Q psy3500 4 CKTCSTLSRPNI-------------SYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERK-H 69 (98)
Q Consensus 4 c~~c~~~~~~~~-------------~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~-~ 69 (98)
|+.||++|+... ..+|.|..|.+.|..+..|..|+..|.. .+.|++|.-+....+.|.+|++. |
T Consensus 210 Cp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn--~ykCplCdmtc~~~ssL~~H~r~rH 287 (467)
T KOG3608|consen 210 CPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN--CYKCPLCDMTCSSASSLTTHIRYRH 287 (467)
T ss_pred cchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh--cccccccccCCCChHHHHHHHHhhh
Confidence 888998886433 2378999999999999999999888774 48899999999999999999874 7
Q ss_pred CCCCCeecCcCcccccChHHHHHHHhhh
Q psy3500 70 TGDKPYICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 70 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
..++||+|..|++.|...++|+.|..+|
T Consensus 288 s~dkpfKCd~Cd~~c~~esdL~kH~~~H 315 (467)
T KOG3608|consen 288 SKDKPFKCDECDTRCVRESDLAKHVQVH 315 (467)
T ss_pred ccCCCccccchhhhhccHHHHHHHHHhc
Confidence 7789999999999999999999998876
No 8
>KOG3623|consensus
Probab=99.53 E-value=2.4e-15 Score=94.43 Aligned_cols=79 Identities=28% Similarity=0.672 Sum_probs=71.1
Q ss_pred CceecCCCCCcCCCHHHHHHHHHHhcCC-------------CceecCCCccccccchhHHHHHHhhCCCCCeecCcCccc
Q psy3500 17 YKYTCYACDYHTLMSEDMKKHMRKHTGE-------------KPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDT 83 (98)
Q Consensus 17 ~~~~c~~C~~~~~~~~~l~~h~~~h~~~-------------~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 83 (98)
.-|.|..|..+|.....|.+|+.+|... +.|.|..|++.|...-.|+.|+++|.|++||.|+.|++.
T Consensus 239 ~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKR 318 (1007)
T KOG3623|consen 239 PNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKR 318 (1007)
T ss_pred CCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccc
Confidence 4588999999999999999999887432 349999999999999999999999999999999999999
Q ss_pred ccChHHHHHHHh
Q psy3500 84 FSSLYLFRNHLQ 95 (98)
Q Consensus 84 f~~~~~l~~H~~ 95 (98)
|.+...+..|+.
T Consensus 319 FSHSGSySSHmS 330 (1007)
T KOG3623|consen 319 FSHSGSYSSHMS 330 (1007)
T ss_pred cccCCccccccc
Confidence 999988888864
No 9
>PHA00733 hypothetical protein
Probab=99.34 E-value=1.2e-12 Score=67.98 Aligned_cols=80 Identities=16% Similarity=0.301 Sum_probs=65.2
Q ss_pred CCceecCCCCCcCCCHHHHHHH--HH---HhcCCCceecCCCccccccchhHHHHHHhhCCCCCeecCcCcccccChHHH
Q psy3500 16 SYKYTCYACDYHTLMSEDMKKH--MR---KHTGEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLF 90 (98)
Q Consensus 16 ~~~~~c~~C~~~~~~~~~l~~h--~~---~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l 90 (98)
.+++.|.+|...|.....|..+ .. .+.+..|+.|+.|++.|.....|..|++.+ +.++.|..|++.|.....|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHH
Confidence 3568899998888777766655 11 234577999999999999999999999876 4579999999999999999
Q ss_pred HHHHhhh
Q psy3500 91 RNHLQSH 97 (98)
Q Consensus 91 ~~H~~~h 97 (98)
..|+...
T Consensus 116 ~~H~~~~ 122 (128)
T PHA00733 116 LDHVCKK 122 (128)
T ss_pred HHHHHHh
Confidence 9998653
No 10
>KOG3608|consensus
Probab=99.31 E-value=8.9e-13 Score=77.36 Aligned_cols=84 Identities=29% Similarity=0.584 Sum_probs=49.7
Q ss_pred cCCCCCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCC--CccccccchhHHHHHHh-hCCC--CCeecCcCccccc
Q psy3500 11 SRPNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEY--CAYSCTQSSALKIHERK-HTGD--KPYICQQCRDTFS 85 (98)
Q Consensus 11 ~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~--c~~~~~~~~~l~~h~~~-~~~~--~~~~C~~C~~~f~ 85 (98)
++++.+++|+|..|+..+...+.|.+|..+|. +..|.|.. |...+.....+..|.+. |.|. .+|.|-.|++.|.
T Consensus 285 ~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft 363 (467)
T KOG3608|consen 285 YRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFT 363 (467)
T ss_pred hhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhc
Confidence 44555666666666666666666666665554 33455544 55555555556666543 2232 2467777777777
Q ss_pred ChHHHHHHHh
Q psy3500 86 SLYLFRNHLQ 95 (98)
Q Consensus 86 ~~~~l~~H~~ 95 (98)
...+|..|++
T Consensus 364 ~G~~L~~HL~ 373 (467)
T KOG3608|consen 364 SGKSLSAHLM 373 (467)
T ss_pred cchhHHHHHH
Confidence 7777777753
No 11
>KOG1074|consensus
Probab=99.31 E-value=3.2e-13 Score=85.96 Aligned_cols=53 Identities=32% Similarity=0.722 Sum_probs=40.1
Q ss_pred CceecCCCccccccchhHHHHHHhhCCCCCeecCcCcccccChHHHHHHHhhh
Q psy3500 45 KPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 45 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
.|-.|.+|.+...-.+.|+-|.+.|+|||||+|..||++|..+.+|..|+-+|
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vH 656 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVH 656 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhccccc
Confidence 35667777777777777777777777777777777777777777777777665
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.21 E-value=8.7e-11 Score=73.41 Aligned_cols=74 Identities=20% Similarity=0.472 Sum_probs=44.6
Q ss_pred CCCccC-CCCCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccchhHHHHHHhhCCCCCeecCcCccccc
Q psy3500 7 CSTLSR-PNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFS 85 (98)
Q Consensus 7 c~~~~~-~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 85 (98)
||..|. ...+.++.|..|+..|. ...|..|+..+. .++.|+ |+..+ ....|..|+..+.+.+++.|+.|+..+.
T Consensus 441 Cg~v~~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 441 CGIVLRVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQ 515 (567)
T ss_pred ccceeeccccccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccc
Confidence 555443 33345566777766664 455666666553 566676 76543 4456666666666667777777766663
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.19 E-value=7.4e-12 Score=55.22 Aligned_cols=39 Identities=26% Similarity=0.492 Sum_probs=19.5
Q ss_pred eecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccc
Q psy3500 19 YTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQS 59 (98)
Q Consensus 19 ~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~ 59 (98)
|+|+.||+.|...+.|..|+++|. +++.|..|++.|...
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~ 44 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRT 44 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccc
Confidence 445555555555555555555544 344555555544433
No 14
>PHA02768 hypothetical protein; Provisional
Probab=99.14 E-value=3e-11 Score=53.30 Aligned_cols=43 Identities=19% Similarity=0.358 Sum_probs=38.9
Q ss_pred ceecCCCccccccchhHHHHHHhhCCCCCeecCcCcccccChHHH
Q psy3500 46 PYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLF 90 (98)
Q Consensus 46 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l 90 (98)
-|.|+.||+.|...++|..|++.|+ ++++|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 3789999999999999999999998 689999999999877654
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.12 E-value=5.3e-10 Score=69.99 Aligned_cols=89 Identities=18% Similarity=0.373 Sum_probs=70.0
Q ss_pred CCCCCCCCccCCC--------CCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCcccccc----------chhHH
Q psy3500 2 YHCKTCSTLSRPN--------ISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQ----------SSALK 63 (98)
Q Consensus 2 ~~c~~c~~~~~~~--------~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~----------~~~l~ 63 (98)
++|+.||+.|... ..+++.|+ |+..+ ....|..|+.+|-..+++.|+.|+..+.. .+.|.
T Consensus 454 ~~C~~Cgk~f~~s~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt 531 (567)
T PLN03086 454 VHCEKCGQAFQQGEMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMS 531 (567)
T ss_pred ccCCCCCCccchHHHHHHHHhcCCCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHH
Confidence 6899999877421 02678999 99755 66889999999999999999999998842 34788
Q ss_pred HHHHhhCCCCCeecCcCcccccChHHHHHHH
Q psy3500 64 IHERKHTGDKPYICQQCRDTFSSLYLFRNHL 94 (98)
Q Consensus 64 ~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 94 (98)
.|.... |.+++.|..||+.+.... +..|+
T Consensus 532 ~HE~~C-G~rt~~C~~Cgk~Vrlrd-m~~H~ 560 (567)
T PLN03086 532 EHESIC-GSRTAPCDSCGRSVMLKE-MDIHQ 560 (567)
T ss_pred HHHHhc-CCcceEccccCCeeeehh-HHHHH
Confidence 888874 899999999998877653 55554
No 16
>PHA00733 hypothetical protein
Probab=99.12 E-value=7.8e-11 Score=61.29 Aligned_cols=53 Identities=23% Similarity=0.331 Sum_probs=46.7
Q ss_pred CCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccchhHHHHHHhh
Q psy3500 15 ISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKH 69 (98)
Q Consensus 15 ~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~ 69 (98)
++.+|.|..|++.|.....|..|+..+ ..++.|..|++.|.....|..|+...
T Consensus 70 ~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~ 122 (128)
T PHA00733 70 AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKK 122 (128)
T ss_pred CCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHh
Confidence 456899999999999999999999865 35799999999999999999998754
No 17
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.10 E-value=1.1e-10 Score=44.44 Aligned_cols=24 Identities=54% Similarity=1.092 Sum_probs=17.1
Q ss_pred HHHHHHhhCCCCCeecCcCccccc
Q psy3500 62 LKIHERKHTGDKPYICQQCRDTFS 85 (98)
Q Consensus 62 l~~h~~~~~~~~~~~C~~C~~~f~ 85 (98)
|..|++.|++++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 566777777777777777777765
No 18
>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=98.92 E-value=1.8e-09 Score=41.04 Aligned_cols=25 Identities=60% Similarity=1.299 Sum_probs=23.0
Q ss_pred HHHHHHHHhcCCCceecCCCccccc
Q psy3500 33 DMKKHMRKHTGEKPYKCEYCAYSCT 57 (98)
Q Consensus 33 ~l~~h~~~h~~~~~~~c~~c~~~~~ 57 (98)
+|..|+++|++++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4789999999999999999999886
No 19
>KOG3993|consensus
Probab=98.81 E-value=8e-10 Score=66.45 Aligned_cols=24 Identities=25% Similarity=0.627 Sum_probs=22.2
Q ss_pred CeecCcCcccccChHHHHHHHhhh
Q psy3500 74 PYICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 74 ~~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
-|.|..|++.|....-|+.|+.+|
T Consensus 356 i~~C~~C~KkFrRqAYLrKHqlth 379 (500)
T KOG3993|consen 356 IFSCHTCGKKFRRQAYLRKHQLTH 379 (500)
T ss_pred eeecHHhhhhhHHHHHHHHhHHhh
Confidence 589999999999999999998776
No 20
>PHA00616 hypothetical protein
Probab=98.68 E-value=9.6e-09 Score=43.37 Aligned_cols=34 Identities=18% Similarity=0.362 Sum_probs=24.8
Q ss_pred ceecCCCCCcCCCHHHHHHHHHHhcCCCceecCC
Q psy3500 18 KYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEY 51 (98)
Q Consensus 18 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~ 51 (98)
+|+|+.||..|.....|..|++.|++++++.+..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 4677777777777777777777777777766654
No 21
>PHA00732 hypothetical protein
Probab=98.56 E-value=6.3e-08 Score=46.34 Aligned_cols=45 Identities=31% Similarity=0.564 Sum_probs=36.2
Q ss_pred ceecCCCCCcCCCHHHHHHHHHH-hcCCCceecCCCccccccchhHHHHHHh
Q psy3500 18 KYTCYACDYHTLMSEDMKKHMRK-HTGEKPYKCEYCAYSCTQSSALKIHERK 68 (98)
Q Consensus 18 ~~~c~~C~~~~~~~~~l~~h~~~-h~~~~~~~c~~c~~~~~~~~~l~~h~~~ 68 (98)
+|.|..|++.|.....|..|++. |.+ +.|+.|++.|.. +..|...
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~~---l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYRR---LNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeCC---hhhhhcc
Confidence 47899999999999999999874 553 579999999884 5667643
No 22
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.53 E-value=1e-07 Score=35.01 Aligned_cols=23 Identities=35% Similarity=0.769 Sum_probs=18.3
Q ss_pred eecCcCcccccChHHHHHHHhhh
Q psy3500 75 YICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 75 ~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
|.|+.|++.|.....|..|++.|
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 57888888888888888888764
No 23
>PHA00616 hypothetical protein
Probab=98.51 E-value=5e-08 Score=41.21 Aligned_cols=34 Identities=12% Similarity=0.143 Sum_probs=29.9
Q ss_pred ceecCCCccccccchhHHHHHHhhCCCCCeecCc
Q psy3500 46 PYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQ 79 (98)
Q Consensus 46 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~ 79 (98)
|+.|+.||+.|.....+..|++.+++++++.|..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 5789999999999999999999999998887754
No 24
>PHA00732 hypothetical protein
Probab=98.45 E-value=2.8e-07 Score=44.16 Aligned_cols=44 Identities=30% Similarity=0.684 Sum_probs=28.2
Q ss_pred ceecCCCccccccchhHHHHHHh-hCCCCCeecCcCcccccChHHHHHHHh
Q psy3500 46 PYKCEYCAYSCTQSSALKIHERK-HTGDKPYICQQCRDTFSSLYLFRNHLQ 95 (98)
Q Consensus 46 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~C~~C~~~f~~~~~l~~H~~ 95 (98)
|+.|..|++.|.....|..|++. |. ++.|+.|++.|.. +..|.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~---l~~H~~ 45 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR---LNQHFY 45 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC---hhhhhc
Confidence 45677777777777777777663 43 2467777777763 445543
No 25
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.27 E-value=1.3e-06 Score=32.10 Aligned_cols=24 Identities=29% Similarity=0.710 Sum_probs=17.0
Q ss_pred eecCcCcccccChHHHHHHHhhhC
Q psy3500 75 YICQQCRDTFSSLYLFRNHLQSHG 98 (98)
Q Consensus 75 ~~C~~C~~~f~~~~~l~~H~~~h~ 98 (98)
|.|+.|++.|.....|..|+++++
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 567888888888888888887663
No 26
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.27 E-value=9.7e-07 Score=33.62 Aligned_cols=24 Identities=50% Similarity=0.987 Sum_probs=19.0
Q ss_pred CeecCcCcccccChHHHHHHHhhh
Q psy3500 74 PYICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 74 ~~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
||.|..|++.|.....|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 577888888888888888888765
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.27 E-value=1.1e-06 Score=32.18 Aligned_cols=22 Identities=32% Similarity=0.727 Sum_probs=13.8
Q ss_pred eecCCCCCcCCCHHHHHHHHHH
Q psy3500 19 YTCYACDYHTLMSEDMKKHMRK 40 (98)
Q Consensus 19 ~~c~~C~~~~~~~~~l~~h~~~ 40 (98)
|+|+.|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4566666666666666666654
No 28
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.21 E-value=3.7e-06 Score=37.43 Aligned_cols=46 Identities=26% Similarity=0.579 Sum_probs=19.7
Q ss_pred eecCCCccccccchhHHHHHHh-hCCC-CCeecCcCcccccChHHHHHHHh
Q psy3500 47 YKCEYCAYSCTQSSALKIHERK-HTGD-KPYICQQCRDTFSSLYLFRNHLQ 95 (98)
Q Consensus 47 ~~c~~c~~~~~~~~~l~~h~~~-~~~~-~~~~C~~C~~~f~~~~~l~~H~~ 95 (98)
|.|+.|++. .+...|..|... |..+ +.+.|+.|...+. .+|..|+.
T Consensus 3 f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~ 50 (54)
T PF05605_consen 3 FTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLN 50 (54)
T ss_pred cCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHH
Confidence 445555552 223445555332 2222 2355555554322 24555544
No 29
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.18 E-value=8e-06 Score=36.35 Aligned_cols=49 Identities=24% Similarity=0.476 Sum_probs=36.9
Q ss_pred ceecCCCCCcCCCHHHHHHHHH-HhcCC-CceecCCCccccccchhHHHHHHhh
Q psy3500 18 KYTCYACDYHTLMSEDMKKHMR-KHTGE-KPYKCEYCAYSCTQSSALKIHERKH 69 (98)
Q Consensus 18 ~~~c~~C~~~~~~~~~l~~h~~-~h~~~-~~~~c~~c~~~~~~~~~l~~h~~~~ 69 (98)
.|.|+.|++ ......|..|.. .|..+ +.+.|++|...+. .+|..|+...
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 478999999 556778999977 45543 5689999998544 4788887754
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.14 E-value=3e-06 Score=42.06 Aligned_cols=72 Identities=26% Similarity=0.423 Sum_probs=19.1
Q ss_pred ecCCCCCcCCCHHHHHHHHHH-hcCCCceecCCCccccccchhHHHHHHhhCCCCCeecCcCcccccChHHHHHHHhhh
Q psy3500 20 TCYACDYHTLMSEDMKKHMRK-HTGEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 20 ~c~~C~~~~~~~~~l~~h~~~-h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
+|..|+..|.....|..|+.. |.-..+ ....+.....+..+.... ....+.|..|++.|.....|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~-----~~~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP-----DQKYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccc-----cccccccccccccccccc-cCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 477888888888888888864 322211 001111222233332221 122588888888888888888888754
No 31
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.89 E-value=1.9e-05 Score=28.76 Aligned_cols=23 Identities=26% Similarity=0.686 Sum_probs=12.8
Q ss_pred eecCCCCCcCCCHHHHHHHHHHh
Q psy3500 19 YTCYACDYHTLMSEDMKKHMRKH 41 (98)
Q Consensus 19 ~~c~~C~~~~~~~~~l~~h~~~h 41 (98)
|.|+.|+..|.....|..|+..+
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 45666666666666666666543
No 32
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.86 E-value=1.7e-05 Score=29.42 Aligned_cols=23 Identities=30% Similarity=0.824 Sum_probs=17.3
Q ss_pred eecCcCcccccChHHHHHHHhhh
Q psy3500 75 YICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 75 ~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
|.|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46777888888888888887755
No 33
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.81 E-value=1.8e-05 Score=30.01 Aligned_cols=21 Identities=19% Similarity=0.493 Sum_probs=10.4
Q ss_pred eecCCCCCcCCCHHHHHHHHH
Q psy3500 19 YTCYACDYHTLMSEDMKKHMR 39 (98)
Q Consensus 19 ~~c~~C~~~~~~~~~l~~h~~ 39 (98)
|+|..|++.|.....|..|++
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~ 22 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKR 22 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHC
T ss_pred CCCCccCCccCChhHHHHHhH
Confidence 445555555555555554443
No 34
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.70 E-value=5.8e-05 Score=32.77 Aligned_cols=31 Identities=29% Similarity=0.408 Sum_probs=15.0
Q ss_pred CCCceecCCCccccccchhHHHHHHhhCCCC
Q psy3500 43 GEKPYKCEYCAYSCTQSSALKIHERKHTGDK 73 (98)
Q Consensus 43 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~ 73 (98)
.+.|..|++|+..+....+|.+|+....+.+
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 3455666666666666666666665554444
No 35
>KOG3993|consensus
Probab=97.66 E-value=5e-06 Score=50.72 Aligned_cols=51 Identities=25% Similarity=0.464 Sum_probs=35.1
Q ss_pred eecCCCccccccchhHHHHHHhhCCCCCeecCcCcccccChHHHHHHHhhh
Q psy3500 47 YKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 47 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
|.|+.|...|...-.|..|.-..-...-|+|++|+++|.-..+|..|+|=|
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWH 318 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWH 318 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhccc
Confidence 777777777777777777753322222377888888888777777777654
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.57 E-value=0.00013 Score=26.84 Aligned_cols=23 Identities=35% Similarity=0.668 Sum_probs=15.0
Q ss_pred eecCCCCCcCCCHHHHHHHHHHh
Q psy3500 19 YTCYACDYHTLMSEDMKKHMRKH 41 (98)
Q Consensus 19 ~~c~~C~~~~~~~~~l~~h~~~h 41 (98)
|.|..|+..|.....+..|+..|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 35666777777776777666644
No 37
>PRK04860 hypothetical protein; Provisional
Probab=97.57 E-value=0.00011 Score=39.88 Aligned_cols=38 Identities=29% Similarity=0.771 Sum_probs=31.0
Q ss_pred ceecCCCccccccchhHHHHHHhhCCCCCeecCcCcccccCh
Q psy3500 46 PYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSL 87 (98)
Q Consensus 46 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 87 (98)
+|.|. |+. ....+..|.++++++++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 58887 887 555678899999999999999999887653
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.50 E-value=0.00012 Score=27.05 Aligned_cols=23 Identities=39% Similarity=0.804 Sum_probs=17.1
Q ss_pred eecCcCcccccChHHHHHHHhhh
Q psy3500 75 YICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 75 ~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
|.|..|+..|.....+..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 56777888888888888877653
No 39
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.45 E-value=4.2e-05 Score=45.38 Aligned_cols=52 Identities=33% Similarity=0.680 Sum_probs=38.0
Q ss_pred CCceecCC--CccccccchhHHHHHHhh-------------------CCCCCeecCcCcccccChHHHHHHHh
Q psy3500 44 EKPYKCEY--CAYSCTQSSALKIHERKH-------------------TGDKPYICQQCRDTFSSLYLFRNHLQ 95 (98)
Q Consensus 44 ~~~~~c~~--c~~~~~~~~~l~~h~~~~-------------------~~~~~~~C~~C~~~f~~~~~l~~H~~ 95 (98)
++||.|++ |.+.|.....|+-|+.-- ...+||+|+.|++.+....-|.-|+.
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 47777766 677777777777776421 12479999999999998888877753
No 40
>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=97.33 E-value=0.00066 Score=29.55 Aligned_cols=33 Identities=21% Similarity=0.360 Sum_probs=22.6
Q ss_pred CCCCceecCCCCCcCCCHHHHHHHHHHhcCCCc
Q psy3500 14 NISYKYTCYACDYHTLMSEDMKKHMRKHTGEKP 46 (98)
Q Consensus 14 ~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~ 46 (98)
..+.|-+|++|+..+.+..+|.+|+....+.+|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 445789999999999999999999987666554
No 41
>PRK04860 hypothetical protein; Provisional
Probab=97.20 E-value=0.00038 Score=37.81 Aligned_cols=40 Identities=25% Similarity=0.623 Sum_probs=33.6
Q ss_pred CceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccch
Q psy3500 17 YKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSS 60 (98)
Q Consensus 17 ~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~ 60 (98)
.+|.|. |+. ....+..|.+++.++++|.|..|+..|....
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 469997 987 5567899999999999999999998876543
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.17 E-value=0.00031 Score=25.94 Aligned_cols=21 Identities=19% Similarity=0.618 Sum_probs=12.5
Q ss_pred eecCCCCCcCCCHHHHHHHHH
Q psy3500 19 YTCYACDYHTLMSEDMKKHMR 39 (98)
Q Consensus 19 ~~c~~C~~~~~~~~~l~~h~~ 39 (98)
|.|.+|+..|.....+..|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 356666666666666666554
No 43
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.08 E-value=0.00021 Score=27.06 Aligned_cols=22 Identities=32% Similarity=0.756 Sum_probs=16.1
Q ss_pred eecCcCcccccChHHHHHHHhh
Q psy3500 75 YICQQCRDTFSSLYLFRNHLQS 96 (98)
Q Consensus 75 ~~C~~C~~~f~~~~~l~~H~~~ 96 (98)
|.|..|++.|.....|..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 5677777777777777777654
No 44
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.87 E-value=0.00035 Score=41.62 Aligned_cols=53 Identities=30% Similarity=0.615 Sum_probs=41.2
Q ss_pred CCCceecCC--CCCcCCCHHHHHHHHHH-h------------------cCCCceecCCCccccccchhHHHHHH
Q psy3500 15 ISYKYTCYA--CDYHTLMSEDMKKHMRK-H------------------TGEKPYKCEYCAYSCTQSSALKIHER 67 (98)
Q Consensus 15 ~~~~~~c~~--C~~~~~~~~~l~~h~~~-h------------------~~~~~~~c~~c~~~~~~~~~l~~h~~ 67 (98)
++++|+|++ |++.+...-.|+-|+.- | ...+||.|.+|++.|.....|+-|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 358999974 77888888888888742 2 12378999999999999998887754
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.77 E-value=0.0024 Score=23.28 Aligned_cols=22 Identities=36% Similarity=1.013 Sum_probs=13.4
Q ss_pred eecCCCCCcCCCHHHHHHHHHHh
Q psy3500 19 YTCYACDYHTLMSEDMKKHMRKH 41 (98)
Q Consensus 19 ~~c~~C~~~~~~~~~l~~h~~~h 41 (98)
|.|+.|+.... ...|..|+..+
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 56777776666 66777776653
No 46
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.52 E-value=0.0034 Score=23.31 Aligned_cols=21 Identities=19% Similarity=0.362 Sum_probs=12.5
Q ss_pred eecCcCcccccChHHHHHHHhh
Q psy3500 75 YICQQCRDTFSSLYLFRNHLQS 96 (98)
Q Consensus 75 ~~C~~C~~~f~~~~~l~~H~~~ 96 (98)
..|+.||+.| ....|..|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3566777777 44446666553
No 47
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=96.44 E-value=0.0052 Score=27.65 Aligned_cols=9 Identities=44% Similarity=1.438 Sum_probs=5.2
Q ss_pred CCeecCcCc
Q psy3500 73 KPYICQQCR 81 (98)
Q Consensus 73 ~~~~C~~C~ 81 (98)
.+|.|+.||
T Consensus 47 ~~Y~CP~CG 55 (59)
T PRK14890 47 NPYTCPKCG 55 (59)
T ss_pred CceECCCCC
Confidence 456666665
No 48
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=96.26 E-value=0.0075 Score=27.12 Aligned_cols=32 Identities=22% Similarity=0.527 Sum_probs=16.2
Q ss_pred CceecCCCccccccchhHHHHHHhhCCCCCeecCcCc
Q psy3500 45 KPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCR 81 (98)
Q Consensus 45 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~ 81 (98)
..|.|+.||.....+-. +-.....+|.|+.||
T Consensus 26 v~F~CPnCGe~~I~Rc~-----~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 26 VKFPCPNCGEVEIYRCA-----KCRKLGNPYRCPKCG 57 (61)
T ss_pred eEeeCCCCCceeeehhh-----hHHHcCCceECCCcC
Confidence 34667777754333221 111224467777775
No 49
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.03 E-value=0.011 Score=29.12 Aligned_cols=24 Identities=29% Similarity=0.714 Sum_probs=20.8
Q ss_pred ceecCCCccccccchhHHHHHHhh
Q psy3500 46 PYKCEYCAYSCTQSSALKIHERKH 69 (98)
Q Consensus 46 ~~~c~~c~~~~~~~~~l~~h~~~~ 69 (98)
.+.|..|+..|.+...|..|+..+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 689999999999999999999864
No 50
>KOG2231|consensus
Probab=95.97 E-value=0.018 Score=38.01 Aligned_cols=92 Identities=23% Similarity=0.349 Sum_probs=50.8
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcCCCHHHHHHHHH-HhcCCCceecCC-------CccccccchhHHHHHHh-hCCC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHTLMSEDMKKHMR-KHTGEKPYKCEY-------CAYSCTQSSALKIHERK-HTGD 72 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~-~h~~~~~~~c~~-------c~~~~~~~~~l~~h~~~-~~~~ 72 (98)
+.|.+|++.+.....+ -.|..| -.|.....|+.|+. .|....-..|.. +.+.|.. ..|..|+.. ..++
T Consensus 100 ~~C~~C~~~~~~~~~~-~~~~~c-~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~-~el~~h~~~gd~d~ 176 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNK-KECLHC-TEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTR-AELNLHLMFGDPDD 176 (669)
T ss_pred hhcCccccchhhhccc-CCCccc-cchhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehH-HHHHHHHhcCCCcc
Confidence 4688888877654432 256677 56777788999985 343321112211 2233333 334555432 1112
Q ss_pred CC----eecCcCcccccChHHHHHHHhh
Q psy3500 73 KP----YICQQCRDTFSSLYLFRNHLQS 96 (98)
Q Consensus 73 ~~----~~C~~C~~~f~~~~~l~~H~~~ 96 (98)
+. -.|..|...|.....|..|++.
T Consensus 177 ~s~rGhp~C~~C~~~fld~~el~rH~~~ 204 (669)
T KOG2231|consen 177 ESCRGHPLCKFCHERFLDDDELYRHLRF 204 (669)
T ss_pred ccccCCccchhhhhhhccHHHHHHhhcc
Confidence 22 3466677777777778777764
No 51
>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=95.91 E-value=0.01 Score=23.57 Aligned_cols=22 Identities=27% Similarity=0.617 Sum_probs=15.1
Q ss_pred CeecCcCcccccChHHHHHHHh
Q psy3500 74 PYICQQCRDTFSSLYLFRNHLQ 95 (98)
Q Consensus 74 ~~~C~~C~~~f~~~~~l~~H~~ 95 (98)
+|.|..|+..|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667777777777777766654
No 52
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=95.75 E-value=0.0065 Score=25.98 Aligned_cols=27 Identities=22% Similarity=0.520 Sum_probs=15.5
Q ss_pred CCCCCCCCccCCCCCC-ceecCCCCCcC
Q psy3500 2 YHCKTCSTLSRPNISY-KYTCYACDYHT 28 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~-~~~c~~C~~~~ 28 (98)
|.|+.||..+.-.... ...|+.||..+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeE
Confidence 6677777655432222 56677776544
No 53
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=95.73 E-value=0.0085 Score=23.76 Aligned_cols=24 Identities=21% Similarity=0.589 Sum_probs=14.9
Q ss_pred CCCCCCCCccCCCCCCceecCCCCC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDY 26 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~ 26 (98)
|+|..||-.+.. .+.+..|+.|+.
T Consensus 2 ~~C~~CGy~y~~-~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDG-EEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECC-CcCCCcCcCCCC
Confidence 677777766543 224566777764
No 54
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=95.59 E-value=0.011 Score=25.18 Aligned_cols=26 Identities=23% Similarity=0.597 Sum_probs=15.2
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCc
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYH 27 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~ 27 (98)
|.|..||..+.-...-...|+.||..
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCce
Confidence 55666666555444445566666644
No 55
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=95.45 E-value=0.0093 Score=23.87 Aligned_cols=24 Identities=17% Similarity=0.466 Sum_probs=13.8
Q ss_pred CCCCCCCCccCCCCCCceecCCCCC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDY 26 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~ 26 (98)
|+|..||....- .+.+..|+.|+.
T Consensus 3 ~~C~~CG~i~~g-~~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEG-EEAPEKCPICGA 26 (34)
T ss_pred EECCCCCCEeEC-CcCCCcCcCCCC
Confidence 567777754431 224556777764
No 56
>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=95.15 E-value=0.031 Score=20.54 Aligned_cols=22 Identities=23% Similarity=0.751 Sum_probs=11.6
Q ss_pred CCCCCCccCCCC-CCceecCCCC
Q psy3500 4 CKTCSTLSRPNI-SYKYTCYACD 25 (98)
Q Consensus 4 c~~c~~~~~~~~-~~~~~c~~C~ 25 (98)
|..||....+-. ...|.|+.||
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 344555444333 4566676665
No 57
>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=95.10 E-value=0.027 Score=21.12 Aligned_cols=22 Identities=23% Similarity=0.626 Sum_probs=10.8
Q ss_pred CCCCCCccCCCCCCceecCCCCCcC
Q psy3500 4 CKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
|+.|++....... .|+.||..|
T Consensus 3 CP~C~~~V~~~~~---~Cp~CG~~F 24 (26)
T PF10571_consen 3 CPECGAEVPESAK---FCPHCGYDF 24 (26)
T ss_pred CCCCcCCchhhcC---cCCCCCCCC
Confidence 5555554433333 256666555
No 58
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.86 E-value=0.043 Score=22.34 Aligned_cols=33 Identities=18% Similarity=0.535 Sum_probs=19.2
Q ss_pred ecCCCccccccchhHHHHHHhhCCCCCeecCcCccccc
Q psy3500 48 KCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFS 85 (98)
Q Consensus 48 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 85 (98)
.|+.|+..|.-... +...+.+..+|+.|+..|.
T Consensus 4 ~CP~C~~~f~v~~~-----~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD-----KLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHH-----HcccCCcEEECCCCCcEee
Confidence 57777776666543 1123334577777776664
No 59
>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=94.82 E-value=0.024 Score=22.36 Aligned_cols=27 Identities=19% Similarity=0.431 Sum_probs=16.5
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
|.|-.||..+.-...-+-.|+.||...
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-SE
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCCeE
Confidence 567778876664444456788887654
No 60
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.53 E-value=0.12 Score=26.55 Aligned_cols=90 Identities=18% Similarity=0.380 Sum_probs=51.6
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcCCCHHHHHHHHHHhc------CCC-------ceecCCCccccccchhHHHHHHh
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHTLMSEDMKKHMRKHT------GEK-------PYKCEYCAYSCTQSSALKIHERK 68 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~------~~~-------~~~c~~c~~~~~~~~~l~~h~~~ 68 (98)
|.|+.|+.- -=++|-+|+.|+-+......|.+..- |. .+. ...|-.|...|........ ..
T Consensus 2 Y~CPrC~sk---vC~LP~~CpiCgLtLVss~HLARSyH-HLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~ 75 (112)
T TIGR00622 2 YFCPQCRAK---VCELPVECPICGLTLILSTHLARSYH-HLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DE 75 (112)
T ss_pred ccCCCCCCC---ccCCCCcCCcCCCEEeccchHHHhhh-ccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cc
Confidence 566666532 23567889999888777766665421 10 011 1237777777765431110 00
Q ss_pred hCCCCCeecCcCcccccChHHHHHHHhhh
Q psy3500 69 HTGDKPYICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 69 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
-.....|.|+.|...|-..-+.-.|...|
T Consensus 76 ~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 76 LKDSHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred cccccceeCCCCCCccccccchhhhhhcc
Confidence 11233589999998887766666666555
No 61
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=94.43 E-value=0.041 Score=28.10 Aligned_cols=34 Identities=21% Similarity=0.432 Sum_probs=19.7
Q ss_pred CCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccc
Q psy3500 15 ISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQS 59 (98)
Q Consensus 15 ~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~ 59 (98)
...+..|+.||..|-. .+..|..|+.||..|...
T Consensus 6 lGtKR~Cp~CG~kFYD-----------Lnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFYD-----------LNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCcccCCCCcchhcc-----------CCCCCccCCCCCCccCcc
Confidence 3445567777766631 223566677777666655
No 62
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.21 E-value=0.0098 Score=36.57 Aligned_cols=62 Identities=29% Similarity=0.508 Sum_probs=48.6
Q ss_pred CceecCCCCCcCCCHHHHHHHHH--HhcCC--CceecC--CCccccccchhHHHHHHhhCCCCCeecC
Q psy3500 17 YKYTCYACDYHTLMSEDMKKHMR--KHTGE--KPYKCE--YCAYSCTQSSALKIHERKHTGDKPYICQ 78 (98)
Q Consensus 17 ~~~~c~~C~~~~~~~~~l~~h~~--~h~~~--~~~~c~--~c~~~~~~~~~l~~h~~~~~~~~~~~C~ 78 (98)
+++.+..|...|.....+..|.. .|.++ +++.|+ .|++.|.....+..|...+.+..++.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 35778888888888888888888 68888 888888 6888888888888888777776655543
No 63
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=94.13 E-value=0.034 Score=30.53 Aligned_cols=11 Identities=45% Similarity=1.069 Sum_probs=6.4
Q ss_pred CCCceecCCCc
Q psy3500 43 GEKPYKCEYCA 53 (98)
Q Consensus 43 ~~~~~~c~~c~ 53 (98)
++-|-.||+|+
T Consensus 146 ge~P~~CPiCg 156 (166)
T COG1592 146 GEAPEVCPICG 156 (166)
T ss_pred CCCCCcCCCCC
Confidence 34556666665
No 64
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=93.78 E-value=0.11 Score=20.97 Aligned_cols=33 Identities=15% Similarity=0.407 Sum_probs=18.7
Q ss_pred eecCCCccccccchhHHHHHHhhCCCCCeecCcCcccc
Q psy3500 47 YKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTF 84 (98)
Q Consensus 47 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 84 (98)
..|+.|+..|.-.... +....+..+|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEe
Confidence 3567777766665432 12223346777777665
No 65
>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=93.67 E-value=0.11 Score=21.07 Aligned_cols=34 Identities=15% Similarity=0.347 Sum_probs=17.6
Q ss_pred eecCCCccccccchhHHHHHHhhCCCCCeecCcCccccc
Q psy3500 47 YKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFS 85 (98)
Q Consensus 47 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 85 (98)
..|+.|+..|.-..... ........|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCEEECCCCCCEEE
Confidence 45677776665554321 11112466777776553
No 66
>KOG1146|consensus
Probab=93.46 E-value=0.028 Score=39.74 Aligned_cols=75 Identities=25% Similarity=0.495 Sum_probs=40.4
Q ss_pred CceecCCCCCcCCCHHHHHHHHHH-hcCCCceecCCCccccccchhHHHHHHhhCCCCCeecCcCcccccChHHHHHHHh
Q psy3500 17 YKYTCYACDYHTLMSEDMKKHMRK-HTGEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLFRNHLQ 95 (98)
Q Consensus 17 ~~~~c~~C~~~~~~~~~l~~h~~~-h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 95 (98)
+.+.|+.|...|.....|..||++ |..... .+|... .....+.+=.....+.++|.|..|...+.....|..|+.
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~---~~c~~g-q~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQS---AYCKAG-QNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccch---hHhHhc-cccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 456677777777766777776664 332211 111110 000000000001123458899999999999888888875
No 67
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=93.38 E-value=0.062 Score=20.67 Aligned_cols=24 Identities=25% Similarity=0.894 Sum_probs=8.9
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCc
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYH 27 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~ 27 (98)
|.|+.|++.... ...|.|.+|+..
T Consensus 1 ~~C~~C~~~~~~--~~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 1 FRCDACGKPIDG--GWFYRCSECDFD 24 (30)
T ss_dssp ---TTTS----S----EEE-TTT---
T ss_pred CcCCcCCCcCCC--CceEECccCCCc
Confidence 467788776554 567889888654
No 68
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.13 E-value=0.016 Score=35.61 Aligned_cols=53 Identities=36% Similarity=0.667 Sum_probs=46.8
Q ss_pred CceecCCCccccccchhHHHHHH--hhCCC--CCeecC--cCcccccChHHHHHHHhhh
Q psy3500 45 KPYKCEYCAYSCTQSSALKIHER--KHTGD--KPYICQ--QCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 45 ~~~~c~~c~~~~~~~~~l~~h~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h 97 (98)
.+..|..|...|.....+..|.+ .|.++ +++.|+ .|++.|.+...+..|..+|
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~ 346 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLH 346 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccc
Confidence 36788899999999999999999 89999 999999 7999999998888887665
No 69
>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=92.83 E-value=0.068 Score=22.39 Aligned_cols=10 Identities=30% Similarity=0.800 Sum_probs=5.1
Q ss_pred eecCCCCCcC
Q psy3500 19 YTCYACDYHT 28 (98)
Q Consensus 19 ~~c~~C~~~~ 28 (98)
|.|..||..|
T Consensus 6 y~C~~Cg~~f 15 (42)
T PF09723_consen 6 YRCEECGHEF 15 (42)
T ss_pred EEeCCCCCEE
Confidence 4555555444
No 70
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=92.76 E-value=0.059 Score=23.42 Aligned_cols=11 Identities=27% Similarity=0.848 Sum_probs=5.8
Q ss_pred ceecCCCCCcC
Q psy3500 18 KYTCYACDYHT 28 (98)
Q Consensus 18 ~~~c~~C~~~~ 28 (98)
.|.|..|+..+
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 45555555544
No 71
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=92.65 E-value=0.093 Score=24.79 Aligned_cols=30 Identities=20% Similarity=0.539 Sum_probs=17.2
Q ss_pred CCCCCCCCCccC---------CCCCCceecC--CCCCcCCC
Q psy3500 1 MYHCKTCSTLSR---------PNISYKYTCY--ACDYHTLM 30 (98)
Q Consensus 1 ~~~c~~c~~~~~---------~~~~~~~~c~--~C~~~~~~ 30 (98)
|+.|+.||.-.+ ...+.-+.|. +||.+|..
T Consensus 1 mm~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 1 MFHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFIT 41 (72)
T ss_pred CccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEE
Confidence 567888885331 1223346676 77776654
No 72
>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=92.54 E-value=0.13 Score=26.96 Aligned_cols=26 Identities=4% Similarity=-0.212 Sum_probs=12.5
Q ss_pred CCCCCCccCCCCCCceecCCCCCcCC
Q psy3500 4 CKTCSTLSRPNISYKYTCYACDYHTL 29 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~~~~~ 29 (98)
|+.||+-|=..++-|-.|+.||..|.
T Consensus 12 Cp~cg~kFYDLnk~p~vcP~cg~~~~ 37 (129)
T TIGR02300 12 CPNTGSKFYDLNRRPAVSPYTGEQFP 37 (129)
T ss_pred CCCcCccccccCCCCccCCCcCCccC
Confidence 44555444444444444555554443
No 73
>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=92.51 E-value=0.23 Score=27.16 Aligned_cols=34 Identities=15% Similarity=0.393 Sum_probs=25.5
Q ss_pred CCCceecCCCccccccchhHHHHHHhhCCCCCeecCcCccccc
Q psy3500 43 GEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFS 85 (98)
Q Consensus 43 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 85 (98)
...-|.|+.|+..|+...++. ..|.|+.||....
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 445688999998888877663 2599999997643
No 74
>KOG2186|consensus
Probab=92.50 E-value=0.13 Score=30.14 Aligned_cols=49 Identities=22% Similarity=0.471 Sum_probs=35.0
Q ss_pred eecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccchhHHHHHHhhC
Q psy3500 19 YTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHT 70 (98)
Q Consensus 19 ~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~ 70 (98)
|.|..||....-+. +..|+..-.+ .-|.|..|+..|.. .....|..--+
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcc
Confidence 78999998776544 5668765444 46899999999988 45677765333
No 75
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=92.33 E-value=0.095 Score=23.33 Aligned_cols=25 Identities=20% Similarity=0.450 Sum_probs=18.4
Q ss_pred CCCCCeecCcCcccccChHHHHHHH
Q psy3500 70 TGDKPYICQQCRDTFSSLYLFRNHL 94 (98)
Q Consensus 70 ~~~~~~~C~~C~~~f~~~~~l~~H~ 94 (98)
-|+.-+.|+.|+..|.......+|.
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHV 37 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHV 37 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHh
Confidence 4566678888888888777777774
No 76
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=92.18 E-value=0.2 Score=19.24 Aligned_cols=22 Identities=23% Similarity=0.605 Sum_probs=16.7
Q ss_pred CCCCCCCCccCCCCCCceecCCCC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
|.|+.|++...... -|.|..|.
T Consensus 1 ~~C~~C~~~~~~~~--~Y~C~~c~ 22 (30)
T PF03107_consen 1 FWCDVCRRKIDGFY--FYHCSECC 22 (30)
T ss_pred CCCCCCCCCcCCCE--eEEeCCCC
Confidence 67888887766544 78888887
No 77
>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=91.69 E-value=0.11 Score=22.66 Aligned_cols=12 Identities=33% Similarity=0.717 Sum_probs=7.5
Q ss_pred ceecCCCCCcCC
Q psy3500 18 KYTCYACDYHTL 29 (98)
Q Consensus 18 ~~~c~~C~~~~~ 29 (98)
.|.|..|+..|.
T Consensus 5 ey~C~~Cg~~fe 16 (52)
T TIGR02605 5 EYRCTACGHRFE 16 (52)
T ss_pred EEEeCCCCCEeE
Confidence 466667766664
No 78
>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=91.47 E-value=0.12 Score=21.13 Aligned_cols=10 Identities=30% Similarity=0.766 Sum_probs=5.4
Q ss_pred eecCCCCCcC
Q psy3500 19 YTCYACDYHT 28 (98)
Q Consensus 19 ~~c~~C~~~~ 28 (98)
|.|..|+..|
T Consensus 6 y~C~~Cg~~f 15 (41)
T smart00834 6 YRCEDCGHTF 15 (41)
T ss_pred EEcCCCCCEE
Confidence 4555555544
No 79
>PHA00626 hypothetical protein
Probab=91.43 E-value=0.32 Score=21.74 Aligned_cols=13 Identities=31% Similarity=0.889 Sum_probs=7.6
Q ss_pred CceecCCCCCcCC
Q psy3500 17 YKYTCYACDYHTL 29 (98)
Q Consensus 17 ~~~~c~~C~~~~~ 29 (98)
-.|+|+.|+..|.
T Consensus 22 nrYkCkdCGY~ft 34 (59)
T PHA00626 22 DDYVCCDCGYNDS 34 (59)
T ss_pred cceEcCCCCCeec
Confidence 3466666666554
No 80
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=91.36 E-value=0.25 Score=21.37 Aligned_cols=25 Identities=24% Similarity=0.837 Sum_probs=13.8
Q ss_pred CCCCCCccCCCCC---CceecCCCCCcC
Q psy3500 4 CKTCSTLSRPNIS---YKYTCYACDYHT 28 (98)
Q Consensus 4 c~~c~~~~~~~~~---~~~~c~~C~~~~ 28 (98)
|+.||.+...... ..+.|+.|+..+
T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCccccccCCCCCEEECCcCCCeE
Confidence 6677765433221 256677777544
No 81
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=91.08 E-value=0.053 Score=31.04 Aligned_cols=12 Identities=17% Similarity=0.642 Sum_probs=9.0
Q ss_pred eecCcCcccccC
Q psy3500 75 YICQQCRDTFSS 86 (98)
Q Consensus 75 ~~C~~C~~~f~~ 86 (98)
+.|+.||.++..
T Consensus 49 ~vCP~CgyA~~~ 60 (214)
T PF09986_consen 49 WVCPHCGYAAFE 60 (214)
T ss_pred EECCCCCCcccc
Confidence 579999977653
No 82
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=91.05 E-value=0.12 Score=27.22 Aligned_cols=25 Identities=36% Similarity=0.768 Sum_probs=19.0
Q ss_pred CCCCCCCC-ccCCCCCCceecCCCCCcC
Q psy3500 2 YHCKTCST-LSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 2 ~~c~~c~~-~~~~~~~~~~~c~~C~~~~ 28 (98)
.+|+.||. +|...|+. -|+.|+..+
T Consensus 29 ~hCp~Cg~PLF~KdG~v--~CPvC~~~~ 54 (131)
T COG1645 29 KHCPKCGTPLFRKDGEV--FCPVCGYRE 54 (131)
T ss_pred hhCcccCCcceeeCCeE--ECCCCCceE
Confidence 47899997 88877775 499998544
No 83
>KOG2893|consensus
Probab=90.93 E-value=0.087 Score=30.66 Aligned_cols=43 Identities=23% Similarity=0.463 Sum_probs=33.2
Q ss_pred eecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccchhHHHH
Q psy3500 19 YTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIH 65 (98)
Q Consensus 19 ~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h 65 (98)
-+|=.|++.|.....|..|++ .+.|.|.+|-+.+.+...|..|
T Consensus 11 pwcwycnrefddekiliqhqk----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred ceeeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceee
Confidence 357789999998888777664 4679999998877766666666
No 84
>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=90.91 E-value=0.25 Score=21.97 Aligned_cols=26 Identities=15% Similarity=0.423 Sum_probs=13.0
Q ss_pred CCCCCCCCccCCCC---CCceecCCCCCc
Q psy3500 2 YHCKTCSTLSRPNI---SYKYTCYACDYH 27 (98)
Q Consensus 2 ~~c~~c~~~~~~~~---~~~~~c~~C~~~ 27 (98)
|+|+.||..+.-.. .....|+.||..
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGae 31 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAE 31 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCE
Confidence 56777776543211 123456666543
No 85
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=90.68 E-value=0.38 Score=26.84 Aligned_cols=33 Identities=21% Similarity=0.515 Sum_probs=23.7
Q ss_pred CCceecCCCccccccchhHHHHHHhhCCCCCeecCcCccccc
Q psy3500 44 EKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFS 85 (98)
Q Consensus 44 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 85 (98)
..-|.|+.|+..|+...++. ..|.|+.||....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 34588999988887776542 2589999987543
No 86
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=90.54 E-value=0.27 Score=17.76 Aligned_cols=20 Identities=20% Similarity=0.723 Sum_probs=11.9
Q ss_pred CCCCCCccCCCCCCceecCCCCC
Q psy3500 4 CKTCSTLSRPNISYKYTCYACDY 26 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~~ 26 (98)
|+.||......... |+.||.
T Consensus 2 Cp~CG~~~~~~~~f---C~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIEDDAKF---CPNCGT 21 (23)
T ss_pred CcccCCCCCCcCcc---hhhhCC
Confidence 66777766554433 666664
No 87
>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=90.51 E-value=0.31 Score=21.32 Aligned_cols=13 Identities=31% Similarity=0.989 Sum_probs=8.8
Q ss_pred CCCCCCCCCccCC
Q psy3500 1 MYHCKTCSTLSRP 13 (98)
Q Consensus 1 ~~~c~~c~~~~~~ 13 (98)
.|+|..||--+..
T Consensus 1 ~y~C~~CgyiYd~ 13 (50)
T cd00730 1 KYECRICGYIYDP 13 (50)
T ss_pred CcCCCCCCeEECC
Confidence 3778888865553
No 88
>KOG2186|consensus
Probab=90.34 E-value=0.3 Score=28.74 Aligned_cols=46 Identities=20% Similarity=0.509 Sum_probs=30.7
Q ss_pred CCCCCCCCccC-CCCC--------CceecCCCCCcCCCHHHHHHHHHHhcCCCcee
Q psy3500 2 YHCKTCSTLSR-PNIS--------YKYTCYACDYHTLMSEDMKKHMRKHTGEKPYK 48 (98)
Q Consensus 2 ~~c~~c~~~~~-~~~~--------~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~ 48 (98)
|.|+.||..-+ +..+ .-|.|-.|+..|-. ..+..|...-+...-|.
T Consensus 4 FtCnvCgEsvKKp~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~kCITEaQKYg 58 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTKCITEAQKYG 58 (276)
T ss_pred EehhhhhhhccccchHHHHHhccCCeeEEeeccccccc-chhhhhhhhcchHHHhh
Confidence 78999997543 2111 45889999999977 66777877655443333
No 89
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=90.22 E-value=0.17 Score=26.92 Aligned_cols=17 Identities=12% Similarity=0.218 Sum_probs=11.5
Q ss_pred CCCceecCCCCCcCCCH
Q psy3500 15 ISYKYTCYACDYHTLMS 31 (98)
Q Consensus 15 ~~~~~~c~~C~~~~~~~ 31 (98)
....+.|..||..|...
T Consensus 67 ~p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 67 EEAVLKCRNCGNEWSLK 83 (135)
T ss_pred cceEEECCCCCCEEecc
Confidence 34567888888776543
No 90
>PF12773 DZR: Double zinc ribbon
Probab=89.99 E-value=0.48 Score=20.34 Aligned_cols=23 Identities=22% Similarity=0.598 Sum_probs=12.3
Q ss_pred CCCCCCccCCCCCCceecCCCCCcCC
Q psy3500 4 CKTCSTLSRPNISYKYTCYACDYHTL 29 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~~~~~ 29 (98)
|+.||+........ |..|+..+.
T Consensus 1 Cp~Cg~~~~~~~~f---C~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKF---CPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccC---ChhhcCChh
Confidence 55666664443332 666665543
No 91
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=89.86 E-value=0.25 Score=24.35 Aligned_cols=11 Identities=18% Similarity=0.634 Sum_probs=5.2
Q ss_pred ceecCCCCCcC
Q psy3500 18 KYTCYACDYHT 28 (98)
Q Consensus 18 ~~~c~~C~~~~ 28 (98)
|-.|..||..|
T Consensus 58 Pa~CkkCGfef 68 (97)
T COG3357 58 PARCKKCGFEF 68 (97)
T ss_pred ChhhcccCccc
Confidence 34455555444
No 92
>PRK04023 DNA polymerase II large subunit; Validated
Probab=89.85 E-value=0.65 Score=32.71 Aligned_cols=21 Identities=24% Similarity=0.709 Sum_probs=12.0
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCc
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYH 27 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~ 27 (98)
..|+.||+.. ..+.|+.||..
T Consensus 627 RfCpsCG~~t-----~~frCP~CG~~ 647 (1121)
T PRK04023 627 RKCPSCGKET-----FYRRCPFCGTH 647 (1121)
T ss_pred ccCCCCCCcC-----CcccCCCCCCC
Confidence 3567777653 33556666644
No 93
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=89.65 E-value=0.33 Score=21.19 Aligned_cols=11 Identities=27% Similarity=0.930 Sum_probs=6.7
Q ss_pred ceecCCCcccc
Q psy3500 46 PYKCEYCAYSC 56 (98)
Q Consensus 46 ~~~c~~c~~~~ 56 (98)
.+.|..|+.++
T Consensus 37 r~~C~~Cgyt~ 47 (50)
T PRK00432 37 RWHCGKCGYTE 47 (50)
T ss_pred cEECCCcCCEE
Confidence 46677776543
No 94
>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=89.47 E-value=0.4 Score=20.40 Aligned_cols=24 Identities=29% Similarity=0.772 Sum_probs=11.6
Q ss_pred CCCCCCCCc--cCCCCCCceecCCCC
Q psy3500 2 YHCKTCSTL--SRPNISYKYTCYACD 25 (98)
Q Consensus 2 ~~c~~c~~~--~~~~~~~~~~c~~C~ 25 (98)
++|+.||.. +.-.....|+|..|.
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~ 44 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACR 44 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCC
Confidence 456666642 112223456666654
No 95
>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=89.40 E-value=0.22 Score=29.39 Aligned_cols=88 Identities=18% Similarity=0.314 Sum_probs=44.8
Q ss_pred CCCCCCccCCCCCCceecCCCCCcCCCHHHHHHHHHH--hcCCCceecCCCccccccc------hhHHHHHHh----hCC
Q psy3500 4 CKTCSTLSRPNISYKYTCYACDYHTLMSEDMKKHMRK--HTGEKPYKCEYCAYSCTQS------SALKIHERK----HTG 71 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~--h~~~~~~~c~~c~~~~~~~------~~l~~h~~~----~~~ 71 (98)
|-+|.+.-=..|..-|+|..|....-....+ .|+.+ ......|.|.-|++.=... -.-..|.+. ...
T Consensus 128 C~EC~R~vw~hGGrif~CsfC~~flCEDDQF-EHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k 206 (314)
T PF06524_consen 128 CIECERGVWDHGGRIFKCSFCDNFLCEDDQF-EHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEK 206 (314)
T ss_pred eeeeecccccCCCeEEEeecCCCeeeccchh-hhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhccccccc
Confidence 3445554445666779999998655444333 34442 2233356666655421110 011123321 223
Q ss_pred CCCeecCcCcccccChHHHHH
Q psy3500 72 DKPYICQQCRDTFSSLYLFRN 92 (98)
Q Consensus 72 ~~~~~C~~C~~~f~~~~~l~~ 92 (98)
.+++.|+.|+........|..
T Consensus 207 ~k~~PCPKCg~et~eTkdLSm 227 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSM 227 (314)
T ss_pred CCCCCCCCCCCccccccccee
Confidence 468899999866555444443
No 96
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=89.04 E-value=0.21 Score=25.76 Aligned_cols=11 Identities=18% Similarity=0.459 Sum_probs=6.0
Q ss_pred ceecCCCCCcC
Q psy3500 18 KYTCYACDYHT 28 (98)
Q Consensus 18 ~~~c~~C~~~~ 28 (98)
...|..|+..|
T Consensus 70 ~~~C~~Cg~~~ 80 (114)
T PRK03681 70 ECWCETCQQYV 80 (114)
T ss_pred EEEcccCCCee
Confidence 35566666543
No 97
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=88.94 E-value=0.23 Score=25.76 Aligned_cols=11 Identities=18% Similarity=0.480 Sum_probs=6.1
Q ss_pred ceecCCCCCcC
Q psy3500 18 KYTCYACDYHT 28 (98)
Q Consensus 18 ~~~c~~C~~~~ 28 (98)
...|..|+..|
T Consensus 71 ~~~C~~Cg~~~ 81 (117)
T PRK00564 71 ELECKDCSHVF 81 (117)
T ss_pred EEEhhhCCCcc
Confidence 35566666544
No 98
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=88.59 E-value=1.1 Score=24.19 Aligned_cols=37 Identities=24% Similarity=0.564 Sum_probs=24.5
Q ss_pred CCceecCCCccccccchhHHHHHHhhCCCCCeecCcCcccc
Q psy3500 44 EKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTF 84 (98)
Q Consensus 44 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 84 (98)
..-|.|+.|+..|.....+.. ... +..|.|+.||...
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEEL 133 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEE
Confidence 345899999988886544322 111 3349999999765
No 99
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=88.11 E-value=0.5 Score=17.49 Aligned_cols=21 Identities=24% Similarity=0.687 Sum_probs=10.5
Q ss_pred CCCCCCCccCCCCCCceecCCCCC
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACDY 26 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~~ 26 (98)
.|+.||........ -|+.||.
T Consensus 4 ~Cp~Cg~~~~~~~~---fC~~CG~ 24 (26)
T PF13248_consen 4 FCPNCGAEIDPDAK---FCPNCGA 24 (26)
T ss_pred CCcccCCcCCcccc---cChhhCC
Confidence 46777773322222 1666654
No 100
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=87.56 E-value=0.84 Score=19.37 Aligned_cols=21 Identities=29% Similarity=0.907 Sum_probs=15.9
Q ss_pred CCCCCCCCccCCCCCCceecCCCC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
|.|+.|++.+. ...|.|..|.
T Consensus 1 ~~C~~C~~~i~---g~r~~C~~C~ 21 (46)
T cd02249 1 YSCDGCLKPIV---GVRYHCLVCE 21 (46)
T ss_pred CCCcCCCCCCc---CCEEECCCCC
Confidence 67999998432 3788998886
No 101
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=87.51 E-value=0.55 Score=25.63 Aligned_cols=34 Identities=21% Similarity=0.435 Sum_probs=21.8
Q ss_pred CCCCCCCCcc---------CC--CCCCceecCCCCCcCCCHHHHH
Q psy3500 2 YHCKTCSTLS---------RP--NISYKYTCYACDYHTLMSEDMK 35 (98)
Q Consensus 2 ~~c~~c~~~~---------~~--~~~~~~~c~~C~~~~~~~~~l~ 35 (98)
.+|+.||.-. .+ .....+.|+.||.+|.....+.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVE 45 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEecc
Confidence 3699999532 12 1223489999999997664443
No 102
>KOG4173|consensus
Probab=87.47 E-value=0.19 Score=28.62 Aligned_cols=73 Identities=21% Similarity=0.492 Sum_probs=45.3
Q ss_pred eecCC--CCCcCCCHHHHHHHHHHhcCCCceecCCCccccccchhHHHHHH----------hhCCCCCeec--CcCcccc
Q psy3500 19 YTCYA--CDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHER----------KHTGDKPYIC--QQCRDTF 84 (98)
Q Consensus 19 ~~c~~--C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~----------~~~~~~~~~C--~~C~~~f 84 (98)
+.|++ |-+.|........|...-.+ -.|..|.+.|.....|..|+. ...|..-|+| ..|+..|
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 44543 33455555555555432222 268888888888887777764 2334445777 4588888
Q ss_pred cChHHHHHHH
Q psy3500 85 SSLYLFRNHL 94 (98)
Q Consensus 85 ~~~~~l~~H~ 94 (98)
....+...|+
T Consensus 157 kT~r~RkdH~ 166 (253)
T KOG4173|consen 157 KTSRDRKDHM 166 (253)
T ss_pred hhhhhhhhHH
Confidence 8887777775
No 103
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=87.43 E-value=0.51 Score=29.92 Aligned_cols=30 Identities=13% Similarity=0.344 Sum_probs=22.9
Q ss_pred CCCCCCCccCCCCCCceecCCCCCcCCCHH
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACDYHTLMSE 32 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~~~~~~~~ 32 (98)
.|+.||...+..|..=|+|+-|+..+....
T Consensus 352 ~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKSAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhhcCCCCcccccccccCCccc
Confidence 588888887777776788888888776543
No 104
>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=87.43 E-value=0.11 Score=26.76 Aligned_cols=13 Identities=15% Similarity=0.311 Sum_probs=7.2
Q ss_pred ceecCCCCCcCCC
Q psy3500 18 KYTCYACDYHTLM 30 (98)
Q Consensus 18 ~~~c~~C~~~~~~ 30 (98)
...|..|+..|..
T Consensus 70 ~~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 70 RARCRDCGHEFEP 82 (113)
T ss_dssp EEEETTTS-EEEC
T ss_pred cEECCCCCCEEec
Confidence 3566667666643
No 105
>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=86.84 E-value=0.42 Score=18.54 Aligned_cols=22 Identities=18% Similarity=0.421 Sum_probs=6.1
Q ss_pred CCCCCCccCCCCCCceecCCCC
Q psy3500 4 CKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
|+.|+..+.=...--+.|+.|+
T Consensus 5 Cp~C~se~~y~D~~~~vCp~C~ 26 (30)
T PF08274_consen 5 CPLCGSEYTYEDGELLVCPECG 26 (30)
T ss_dssp -TTT-----EE-SSSEEETTTT
T ss_pred CCCCCCcceeccCCEEeCCccc
Confidence 4444443332233334444443
No 106
>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=86.77 E-value=0.51 Score=21.77 Aligned_cols=23 Identities=17% Similarity=0.443 Sum_probs=6.4
Q ss_pred CCCCCCccCCCCCCceecCCCCCc
Q psy3500 4 CKTCSTLSRPNISYKYTCYACDYH 27 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~~~ 27 (98)
|..|++.|.- ....+.|..||..
T Consensus 12 C~~C~~~F~~-~~rrhhCr~CG~~ 34 (69)
T PF01363_consen 12 CMICGKKFSL-FRRRHHCRNCGRV 34 (69)
T ss_dssp -TTT--B-BS-SS-EEE-TTT--E
T ss_pred CcCcCCcCCC-ceeeEccCCCCCE
Confidence 4445555522 2334445555443
No 107
>KOG3507|consensus
Probab=86.75 E-value=0.34 Score=21.83 Aligned_cols=9 Identities=33% Similarity=1.080 Sum_probs=4.8
Q ss_pred ceecCCCcc
Q psy3500 46 PYKCEYCAY 54 (98)
Q Consensus 46 ~~~c~~c~~ 54 (98)
...|..||.
T Consensus 37 ~irCReCG~ 45 (62)
T KOG3507|consen 37 VIRCRECGY 45 (62)
T ss_pred cEehhhcch
Confidence 455555553
No 108
>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=86.53 E-value=1.9 Score=19.79 Aligned_cols=14 Identities=14% Similarity=0.800 Sum_probs=8.0
Q ss_pred CceecCCCcccccc
Q psy3500 45 KPYKCEYCAYSCTQ 58 (98)
Q Consensus 45 ~~~~c~~c~~~~~~ 58 (98)
..+.|+.||.....
T Consensus 45 r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 45 RVFTCPNCGFEMDR 58 (69)
T ss_pred ceEEcCCCCCEECc
Confidence 34666666655443
No 109
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=86.42 E-value=1.2 Score=18.56 Aligned_cols=21 Identities=19% Similarity=0.404 Sum_probs=9.6
Q ss_pred CeecCcCcccccC----hHHHHHHH
Q psy3500 74 PYICQQCRDTFSS----LYLFRNHL 94 (98)
Q Consensus 74 ~~~C~~C~~~f~~----~~~l~~H~ 94 (98)
...|..|++.+.. .+.|..|+
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 3556666655443 24566665
No 110
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=86.37 E-value=0.45 Score=25.16 Aligned_cols=26 Identities=15% Similarity=0.356 Sum_probs=19.7
Q ss_pred CCCCCCCCCccCCCC-CCceecCCCCC
Q psy3500 1 MYHCKTCSTLSRPNI-SYKYTCYACDY 26 (98)
Q Consensus 1 ~~~c~~c~~~~~~~~-~~~~~c~~C~~ 26 (98)
|+.|-.||+.|.... +..--|+.||-
T Consensus 1 PH~Ct~Cg~~f~dgs~eil~GCP~CGg 27 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEILSGCPECGG 27 (131)
T ss_pred CcccCcCCCCcCCCcHHHHccCcccCC
Confidence 789999999998655 44455888873
No 111
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=85.53 E-value=1.1 Score=16.65 Aligned_cols=19 Identities=26% Similarity=0.513 Sum_probs=11.2
Q ss_pred ecCcCcccccChHHHHHHHh
Q psy3500 76 ICQQCRDTFSSLYLFRNHLQ 95 (98)
Q Consensus 76 ~C~~C~~~f~~~~~l~~H~~ 95 (98)
.|+.|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 466666665 4455666654
No 112
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=85.47 E-value=1.1 Score=19.97 Aligned_cols=25 Identities=16% Similarity=0.410 Sum_probs=14.8
Q ss_pred CCCCCCCccCCCCCCceecCCCCCcC
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
.|+.||+-|+..++. -.|++|+-.+
T Consensus 7 ~C~~Cg~~~~~~dDi-VvCp~Cgapy 31 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDI-VVCPECGAPY 31 (54)
T ss_pred cChhhCCcccCCCCE-EECCCCCCcc
Confidence 466777766665553 3566666443
No 113
>PRK05978 hypothetical protein; Provisional
Probab=85.38 E-value=0.82 Score=24.82 Aligned_cols=26 Identities=27% Similarity=0.524 Sum_probs=13.3
Q ss_pred CCCCCCC--ccCCCCCCceecCCCCCcC
Q psy3500 3 HCKTCST--LSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 3 ~c~~c~~--~~~~~~~~~~~c~~C~~~~ 28 (98)
.|+.||+ +|+--.+..-.|+.|+..|
T Consensus 35 rCP~CG~G~LF~g~Lkv~~~C~~CG~~~ 62 (148)
T PRK05978 35 RCPACGEGKLFRAFLKPVDHCAACGEDF 62 (148)
T ss_pred cCCCCCCCcccccccccCCCccccCCcc
Confidence 4666664 3443333444566666554
No 114
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=85.23 E-value=0.65 Score=26.00 Aligned_cols=27 Identities=26% Similarity=0.647 Sum_probs=18.8
Q ss_pred CCCCCCC--ccCCCCCC-------------ceecCCCCCcCC
Q psy3500 3 HCKTCST--LSRPNISY-------------KYTCYACDYHTL 29 (98)
Q Consensus 3 ~c~~c~~--~~~~~~~~-------------~~~c~~C~~~~~ 29 (98)
.|+-||. .|..+|.. -|+|..|+.++.
T Consensus 19 ~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~Cd~tWN 60 (203)
T COG4332 19 RCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTHCDYTWN 60 (203)
T ss_pred hCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeeccCCccc
Confidence 4788884 45555542 399999998874
No 115
>KOG1146|consensus
Probab=84.87 E-value=0.19 Score=35.95 Aligned_cols=20 Identities=25% Similarity=0.486 Sum_probs=13.2
Q ss_pred cCcCcccccChHHHHHHHhh
Q psy3500 77 CQQCRDTFSSLYLFRNHLQS 96 (98)
Q Consensus 77 C~~C~~~f~~~~~l~~H~~~ 96 (98)
|..|...|.....|..|+++
T Consensus 1331 c~~c~~~~~~~~alqihm~~ 1350 (1406)
T KOG1146|consen 1331 CLACEVLLSGREALQIHMRS 1350 (1406)
T ss_pred chHHHhhcchhHHHHHHHHH
Confidence 66666666666666666653
No 116
>PF14353 CpXC: CpXC protein
Probab=84.39 E-value=1.1 Score=23.50 Aligned_cols=10 Identities=20% Similarity=0.557 Sum_probs=6.3
Q ss_pred CCCCCCCccC
Q psy3500 3 HCKTCSTLSR 12 (98)
Q Consensus 3 ~c~~c~~~~~ 12 (98)
.|+.||..|.
T Consensus 3 tCP~C~~~~~ 12 (128)
T PF14353_consen 3 TCPHCGHEFE 12 (128)
T ss_pred CCCCCCCeeE
Confidence 4777776543
No 117
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=84.36 E-value=1.7 Score=18.14 Aligned_cols=26 Identities=15% Similarity=0.226 Sum_probs=14.2
Q ss_pred CCCCCCCccCCCCCCceecCCCCCcCCC
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACDYHTLM 30 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~~~~~~ 30 (98)
+|+.|-+.+ +.+.++.-..|+..|-.
T Consensus 1 ~C~~C~~~~--~~~~~~~l~~CgH~~C~ 26 (44)
T PF14634_consen 1 HCNICFEKY--SEERRPRLTSCGHIFCE 26 (44)
T ss_pred CCcCcCccc--cCCCCeEEcccCCHHHH
Confidence 366666666 33334555566666543
No 118
>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=84.34 E-value=0.41 Score=20.65 Aligned_cols=10 Identities=30% Similarity=0.992 Sum_probs=5.7
Q ss_pred CCCCCCCCcc
Q psy3500 2 YHCKTCSTLS 11 (98)
Q Consensus 2 ~~c~~c~~~~ 11 (98)
|+|..||.-+
T Consensus 2 y~C~~CgyvY 11 (47)
T PF00301_consen 2 YQCPVCGYVY 11 (47)
T ss_dssp EEETTTSBEE
T ss_pred cCCCCCCEEE
Confidence 5666666433
No 119
>KOG1280|consensus
Probab=84.32 E-value=2.3 Score=26.41 Aligned_cols=37 Identities=22% Similarity=0.516 Sum_probs=23.7
Q ss_pred CceecCCCCCcCCCHHHHHHHHHH-hcCC-CceecCCCc
Q psy3500 17 YKYTCYACDYHTLMSEDMKKHMRK-HTGE-KPYKCEYCA 53 (98)
Q Consensus 17 ~~~~c~~C~~~~~~~~~l~~h~~~-h~~~-~~~~c~~c~ 53 (98)
..|+|+.|+++--....+..|... |... -...|++|+
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 358888888877777777777764 3221 224566665
No 120
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=84.29 E-value=1.6 Score=19.31 Aligned_cols=41 Identities=20% Similarity=0.499 Sum_probs=22.9
Q ss_pred CceecCC--CccccccchhHHHHHHhhCCCCCeecCc----CcccccC
Q psy3500 45 KPYKCEY--CAYSCTQSSALKIHERKHTGDKPYICQQ----CRDTFSS 86 (98)
Q Consensus 45 ~~~~c~~--c~~~~~~~~~l~~h~~~~~~~~~~~C~~----C~~~f~~ 86 (98)
.+..|+. |...+. ...|..|....-..++..|+. |...+..
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEEH
T ss_pred CEeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccch
Confidence 3456766 434343 456888888666667788888 7765543
No 121
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=83.92 E-value=1.7 Score=17.91 Aligned_cols=12 Identities=25% Similarity=0.501 Sum_probs=7.7
Q ss_pred ceecCCCCCcCC
Q psy3500 18 KYTCYACDYHTL 29 (98)
Q Consensus 18 ~~~c~~C~~~~~ 29 (98)
-|.|..|+..+.
T Consensus 28 fy~C~~C~~~w~ 39 (40)
T smart00440 28 FYVCTKCGHRWR 39 (40)
T ss_pred EEEeCCCCCEeC
Confidence 377777776553
No 122
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=83.91 E-value=2.4 Score=28.68 Aligned_cols=25 Identities=24% Similarity=0.564 Sum_probs=17.0
Q ss_pred CCCCCCCCCccCCCCCCceecCCCCCcC
Q psy3500 1 MYHCKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 1 ~~~c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
|-.|+.||.......+. |..||..+
T Consensus 1 M~~Cp~Cg~~n~~~akF---C~~CG~~l 25 (645)
T PRK14559 1 MLICPQCQFENPNNNRF---CQKCGTSL 25 (645)
T ss_pred CCcCCCCCCcCCCCCcc---ccccCCCC
Confidence 45788898876655443 77777655
No 123
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=83.90 E-value=1.1 Score=19.32 Aligned_cols=21 Identities=29% Similarity=0.534 Sum_probs=11.1
Q ss_pred eecCcCcccccCh-----HHHHHHHh
Q psy3500 75 YICQQCRDTFSSL-----YLFRNHLQ 95 (98)
Q Consensus 75 ~~C~~C~~~f~~~-----~~l~~H~~ 95 (98)
-.|..|++.+... +.|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 3455555554332 45666665
No 124
>COG1773 Rubredoxin [Energy production and conversion]
Probab=83.76 E-value=0.72 Score=20.60 Aligned_cols=12 Identities=25% Similarity=0.930 Sum_probs=8.1
Q ss_pred CCCCCCCCccCC
Q psy3500 2 YHCKTCSTLSRP 13 (98)
Q Consensus 2 ~~c~~c~~~~~~ 13 (98)
|+|..||.-+..
T Consensus 4 ~~C~~CG~vYd~ 15 (55)
T COG1773 4 WRCSVCGYVYDP 15 (55)
T ss_pred eEecCCceEecc
Confidence 677777766653
No 125
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=83.70 E-value=0.57 Score=24.13 Aligned_cols=11 Identities=18% Similarity=0.588 Sum_probs=6.3
Q ss_pred ceecCCCCCcC
Q psy3500 18 KYTCYACDYHT 28 (98)
Q Consensus 18 ~~~c~~C~~~~ 28 (98)
...|..|+..|
T Consensus 70 ~~~C~~Cg~~~ 80 (113)
T PRK12380 70 QAWCWDCSQVV 80 (113)
T ss_pred EEEcccCCCEE
Confidence 35566666554
No 126
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=83.54 E-value=1.1 Score=27.47 Aligned_cols=24 Identities=33% Similarity=0.498 Sum_probs=16.5
Q ss_pred CeecCcCcccccChHHHHHHHhhh
Q psy3500 74 PYICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 74 ~~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
.|.|+.|...|-..-+.-.|...|
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHHHh
Confidence 588888888887666655555443
No 127
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=83.41 E-value=0.37 Score=25.57 Aligned_cols=13 Identities=23% Similarity=0.567 Sum_probs=7.0
Q ss_pred CceecCCCCCcCC
Q psy3500 17 YKYTCYACDYHTL 29 (98)
Q Consensus 17 ~~~~c~~C~~~~~ 29 (98)
+-|+|..|..+..
T Consensus 79 ~lYeCnIC~etS~ 91 (140)
T PF05290_consen 79 KLYECNICKETSA 91 (140)
T ss_pred CceeccCcccccc
Confidence 4566666655443
No 128
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=83.14 E-value=0.87 Score=19.01 Aligned_cols=25 Identities=16% Similarity=0.445 Sum_probs=11.7
Q ss_pred CCCCCCCCccC--CCCCCceecCCCCC
Q psy3500 2 YHCKTCSTLSR--PNISYKYTCYACDY 26 (98)
Q Consensus 2 ~~c~~c~~~~~--~~~~~~~~c~~C~~ 26 (98)
|+|+.||.... ....-.+.|+.||.
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCC
Confidence 45666665321 22223346666654
No 129
>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=83.06 E-value=0.66 Score=23.97 Aligned_cols=12 Identities=17% Similarity=0.465 Sum_probs=6.9
Q ss_pred ceecCCCCCcCC
Q psy3500 18 KYTCYACDYHTL 29 (98)
Q Consensus 18 ~~~c~~C~~~~~ 29 (98)
...|..|+..|.
T Consensus 70 ~~~C~~Cg~~~~ 81 (115)
T TIGR00100 70 ECECEDCSEEVS 81 (115)
T ss_pred EEEcccCCCEEe
Confidence 356666665553
No 130
>KOG2785|consensus
Probab=82.83 E-value=1.7 Score=27.30 Aligned_cols=77 Identities=19% Similarity=0.352 Sum_probs=41.0
Q ss_pred eecCCCCCcCCCHHHHHHHHHH--hc---CCCc-eecCCCccccccchhHHHHHH---hhCCCCCeecCcCcccccChHH
Q psy3500 19 YTCYACDYHTLMSEDMKKHMRK--HT---GEKP-YKCEYCAYSCTQSSALKIHER---KHTGDKPYICQQCRDTFSSLYL 89 (98)
Q Consensus 19 ~~c~~C~~~~~~~~~l~~h~~~--h~---~~~~-~~c~~c~~~~~~~~~l~~h~~---~~~~~~~~~C~~C~~~f~~~~~ 89 (98)
|+|..|...|........|+++ |. .++- -..++....|........-.. ...++-++.|..|.+.|.....
T Consensus 4 ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~a 83 (390)
T KOG2785|consen 4 FTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPKA 83 (390)
T ss_pred ceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChhh
Confidence 6788888888887777777764 21 1111 112222233333221111111 1233446778888888887777
Q ss_pred HHHHHh
Q psy3500 90 FRNHLQ 95 (98)
Q Consensus 90 l~~H~~ 95 (98)
...|+.
T Consensus 84 ~~~hl~ 89 (390)
T KOG2785|consen 84 HENHLK 89 (390)
T ss_pred HHHHHH
Confidence 666654
No 131
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=82.66 E-value=2.3 Score=31.00 Aligned_cols=21 Identities=29% Similarity=0.702 Sum_probs=11.1
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCc
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYH 27 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~ 27 (98)
+.|+.||..... ..|+.||..
T Consensus 668 rkCPkCG~~t~~-----~fCP~CGs~ 688 (1337)
T PRK14714 668 RRCPSCGTETYE-----NRCPDCGTH 688 (1337)
T ss_pred EECCCCCCcccc-----ccCcccCCc
Confidence 467777764211 146666543
No 132
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=81.82 E-value=1.2 Score=24.16 Aligned_cols=8 Identities=25% Similarity=0.746 Sum_probs=4.2
Q ss_pred eecCCCCC
Q psy3500 19 YTCYACDY 26 (98)
Q Consensus 19 ~~c~~C~~ 26 (98)
|.|..||.
T Consensus 113 l~C~~Cg~ 120 (146)
T PF07295_consen 113 LVCENCGH 120 (146)
T ss_pred EecccCCC
Confidence 55555554
No 133
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=81.65 E-value=2.1 Score=18.50 Aligned_cols=22 Identities=27% Similarity=0.866 Sum_probs=15.3
Q ss_pred CCCCCCCCccCCCCCCceecCCCC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
|.|+.|+..- .....|.|..|.
T Consensus 1 y~Cd~C~~~p--I~G~R~~C~~C~ 22 (48)
T cd02341 1 FKCDSCGIEP--IPGTRYHCSECD 22 (48)
T ss_pred CCCCCCCCCc--cccceEECCCCC
Confidence 6788888732 225678888886
No 134
>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=80.77 E-value=1.1 Score=17.97 Aligned_cols=24 Identities=17% Similarity=0.407 Sum_probs=9.2
Q ss_pred CCCCCCCccCCCCC-CceecCCCCC
Q psy3500 3 HCKTCSTLSRPNIS-YKYTCYACDY 26 (98)
Q Consensus 3 ~c~~c~~~~~~~~~-~~~~c~~C~~ 26 (98)
+|.+||+.|-.+.- ..|.+.+|++
T Consensus 5 ~C~eC~~~f~dSyL~~~F~~~VCD~ 29 (34)
T PF01286_consen 5 KCDECGKPFMDSYLLNNFDLPVCDK 29 (34)
T ss_dssp E-TTT--EES-SSCCCCTS-S--TT
T ss_pred hHhHhCCHHHHHHHHHhCCcccccc
Confidence 46777777665443 2455555543
No 135
>KOG4167|consensus
Probab=80.60 E-value=0.38 Score=32.57 Aligned_cols=25 Identities=20% Similarity=0.562 Sum_probs=22.0
Q ss_pred CeecCcCcccccChHHHHHHHhhhC
Q psy3500 74 PYICQQCRDTFSSLYLFRNHLQSHG 98 (98)
Q Consensus 74 ~~~C~~C~~~f~~~~~l~~H~~~h~ 98 (98)
-|.|.+|++.|..--.+..|+++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4899999999998888999998873
No 136
>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=80.41 E-value=1.5 Score=22.46 Aligned_cols=29 Identities=17% Similarity=0.348 Sum_probs=20.3
Q ss_pred CCCCCCCccCCCCCCceecCCCCCcCCCH
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACDYHTLMS 31 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~~~~~~~ 31 (98)
.|+.|+..+.-....-|.|++|+..+...
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccccccc
Confidence 47777777765555568888888777544
No 137
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=80.40 E-value=0.87 Score=18.72 Aligned_cols=11 Identities=27% Similarity=0.899 Sum_probs=6.7
Q ss_pred CCCCCCCCCcc
Q psy3500 1 MYHCKTCSTLS 11 (98)
Q Consensus 1 ~~~c~~c~~~~ 11 (98)
||+|+.|+..|
T Consensus 12 ~f~C~~C~~~F 22 (39)
T smart00154 12 GFKCRHCGNLF 22 (39)
T ss_pred CeECCccCCcc
Confidence 46666666554
No 138
>PRK10220 hypothetical protein; Provisional
Probab=80.03 E-value=2.1 Score=21.97 Aligned_cols=29 Identities=21% Similarity=0.370 Sum_probs=20.0
Q ss_pred CCCCCCCccCCCCCCceecCCCCCcCCCH
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACDYHTLMS 31 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~~~~~~~ 31 (98)
.|+.|+..+.-...-.|.|++|+.-+...
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCcCCcc
Confidence 47777777765555568888888766544
No 139
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=79.27 E-value=0.68 Score=23.39 Aligned_cols=26 Identities=15% Similarity=0.379 Sum_probs=17.0
Q ss_pred CCCCCCCCCccCC-CCCCceecCCCCC
Q psy3500 1 MYHCKTCSTLSRP-NISYKYTCYACDY 26 (98)
Q Consensus 1 ~~~c~~c~~~~~~-~~~~~~~c~~C~~ 26 (98)
|+.|-.||+.|.. +.+..--|+.||.
T Consensus 2 pH~CtrCG~vf~~g~~~il~GCp~CG~ 28 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEILSGCPKCGC 28 (112)
T ss_pred CceecccccccccccHHHHccCccccc
Confidence 6778888888876 3334455777763
No 140
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=78.84 E-value=1.5 Score=23.94 Aligned_cols=35 Identities=26% Similarity=0.760 Sum_probs=23.8
Q ss_pred CceecCCCccccccchhHHHHHHhhCCCCCeecCcCcccc
Q psy3500 45 KPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTF 84 (98)
Q Consensus 45 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 84 (98)
-+|.|. |+..|.+. ..|-..-.|+ .|.|..|+...
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gkL 150 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGKL 150 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-eEEeccCCceE
Confidence 468888 88876653 3444555666 79999997543
No 141
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=78.58 E-value=3 Score=17.32 Aligned_cols=20 Identities=25% Similarity=1.014 Sum_probs=14.2
Q ss_pred CCCCCCCCccCCCCCCceecCCCC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
|.|+.|+.. .+..+.|.+|+
T Consensus 1 y~C~~C~~~----~~~r~~C~~C~ 20 (41)
T cd02337 1 YTCNECKHH----VETRWHCTVCE 20 (41)
T ss_pred CcCCCCCCc----CCCceECCCCc
Confidence 578888661 23788888886
No 142
>KOG3408|consensus
Probab=78.29 E-value=1.9 Score=22.61 Aligned_cols=26 Identities=19% Similarity=0.606 Sum_probs=19.1
Q ss_pred CCCCeecCcCcccccChHHHHHHHhh
Q psy3500 71 GDKPYICQQCRDTFSSLYLFRNHLQS 96 (98)
Q Consensus 71 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 96 (98)
|.-.|.|..|.+-|.....|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 33357888888888888888888664
No 143
>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=78.00 E-value=2.5 Score=22.56 Aligned_cols=21 Identities=38% Similarity=0.912 Sum_probs=9.9
Q ss_pred CeecCcCcccccChHHHHHHHhhh
Q psy3500 74 PYICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 74 ~~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
...|-+||+.|... .+|++.|
T Consensus 72 ~i~clecGk~~k~L---krHL~~~ 92 (132)
T PF05443_consen 72 YIICLECGKKFKTL---KRHLRTH 92 (132)
T ss_dssp -EE-TBT--EESBH---HHHHHHT
T ss_pred eeEEccCCcccchH---HHHHHHc
Confidence 35666677666553 5565555
No 144
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=77.63 E-value=2.9 Score=20.60 Aligned_cols=33 Identities=24% Similarity=0.443 Sum_probs=19.3
Q ss_pred ceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccch
Q psy3500 18 KYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSS 60 (98)
Q Consensus 18 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~ 60 (98)
+|.|+.|++.- ..+ .+..-+.|..|+..|.-..
T Consensus 35 ~~~Cp~C~~~~--------VkR--~a~GIW~C~kCg~~fAGga 67 (89)
T COG1997 35 KHVCPFCGRTT--------VKR--IATGIWKCRKCGAKFAGGA 67 (89)
T ss_pred CCcCCCCCCcc--------eee--eccCeEEcCCCCCeecccc
Confidence 47788887541 111 1223477888887776543
No 145
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=77.22 E-value=3.7 Score=17.68 Aligned_cols=22 Identities=32% Similarity=0.760 Sum_probs=15.5
Q ss_pred CCCCCCCCccCCCCCCceecCCCC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
|.|+.|++... +...|+|.+|.
T Consensus 1 ~~Cd~C~~~~~--~g~r~~C~~C~ 22 (49)
T cd02335 1 YHCDYCSKDIT--GTIRIKCAECP 22 (49)
T ss_pred CCCCCcCCCCC--CCcEEECCCCC
Confidence 56888887543 44778888885
No 146
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=77.12 E-value=0.1 Score=34.96 Aligned_cols=56 Identities=21% Similarity=0.476 Sum_probs=34.5
Q ss_pred cCCCCCcCCCHHHHHHHHHHhcCCCc-eecCCCccccccchhHHHHHHhhCCCCCeecCcCccc
Q psy3500 21 CYACDYHTLMSEDMKKHMRKHTGEKP-YKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDT 83 (98)
Q Consensus 21 c~~C~~~~~~~~~l~~h~~~h~~~~~-~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 83 (98)
|+.||.+|.....|.=. +.++.=.. --|+.|.+.|....+. +.| ..|..|+.||-.
T Consensus 126 CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~nR----RfH--AQp~aCp~CGP~ 182 (750)
T COG0068 126 CTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLNR----RFH--AQPIACPKCGPH 182 (750)
T ss_pred cCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCcccc----ccc--cccccCcccCCC
Confidence 88999988765554311 12222122 3488888888777542 333 347899999863
No 147
>KOG2893|consensus
Probab=77.11 E-value=0.5 Score=27.68 Aligned_cols=39 Identities=23% Similarity=0.436 Sum_probs=28.9
Q ss_pred ecCCCccccccchhHHHHHHhhCCCCCeecCcCcccccChHHH
Q psy3500 48 KCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSLYLF 90 (98)
Q Consensus 48 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l 90 (98)
.|=+|++.|.....|..|++ .+-|+|-.|-+......-|
T Consensus 12 wcwycnrefddekiliqhqk----akhfkchichkkl~sgpgl 50 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGL 50 (341)
T ss_pred eeeecccccchhhhhhhhhh----hccceeeeehhhhccCCCc
Confidence 46689999999988888876 3458999998765544333
No 148
>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=76.70 E-value=2 Score=17.57 Aligned_cols=11 Identities=27% Similarity=0.658 Sum_probs=7.7
Q ss_pred ceecCCCCCcC
Q psy3500 18 KYTCYACDYHT 28 (98)
Q Consensus 18 ~~~c~~C~~~~ 28 (98)
-|.|..|+..|
T Consensus 28 fy~C~~C~~~w 38 (39)
T PF01096_consen 28 FYVCCNCGHRW 38 (39)
T ss_dssp EEEESSSTEEE
T ss_pred EEEeCCCCCee
Confidence 37888887654
No 149
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=76.55 E-value=2.5 Score=22.40 Aligned_cols=15 Identities=20% Similarity=0.594 Sum_probs=9.8
Q ss_pred CCceecCCCCCcCCC
Q psy3500 16 SYKYTCYACDYHTLM 30 (98)
Q Consensus 16 ~~~~~c~~C~~~~~~ 30 (98)
...|.|+.|+++|..
T Consensus 51 ~qRyrC~~C~~tf~~ 65 (129)
T COG3677 51 HQRYKCKSCGSTFTV 65 (129)
T ss_pred ccccccCCcCcceee
Confidence 446777777777643
No 150
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=76.35 E-value=2.8 Score=18.36 Aligned_cols=27 Identities=15% Similarity=0.282 Sum_probs=14.8
Q ss_pred CCCCCCCccCCCCCCceecCCCCCcCCC
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACDYHTLM 30 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~~~~~~ 30 (98)
.|..|++.|.. ....+.|..||..|-.
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 35666665554 2334556666665543
No 151
>KOG2807|consensus
Probab=76.13 E-value=4.6 Score=25.02 Aligned_cols=22 Identities=18% Similarity=0.398 Sum_probs=14.4
Q ss_pred CCceecCCCCCcCCCHHHHHHH
Q psy3500 16 SYKYTCYACDYHTLMSEDMKKH 37 (98)
Q Consensus 16 ~~~~~c~~C~~~~~~~~~l~~h 37 (98)
.+|-+|+.|+-+......|.+-
T Consensus 288 sLP~eCpiC~ltLVss~hLARS 309 (378)
T KOG2807|consen 288 SLPIECPICSLTLVSSPHLARS 309 (378)
T ss_pred cCCccCCccceeEecchHHHHH
Confidence 3567788888776666666543
No 152
>KOG2593|consensus
Probab=76.05 E-value=5.4 Score=25.64 Aligned_cols=37 Identities=22% Similarity=0.465 Sum_probs=24.2
Q ss_pred CCCceecCCCccccccchhHHHHHHhhCCCCCeecCcCcc
Q psy3500 43 GEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRD 82 (98)
Q Consensus 43 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 82 (98)
....|.|+.|.+.|.....+ +......-.|.|..|+.
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~---~L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEAL---QLLDNETGEFHCENCGG 161 (436)
T ss_pred ccccccCCccccchhhhHHH---HhhcccCceEEEecCCC
Confidence 34568899999888876543 23333233588888874
No 153
>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=75.41 E-value=3.2 Score=20.83 Aligned_cols=26 Identities=31% Similarity=0.821 Sum_probs=19.2
Q ss_pred CCCCCCccCCCCCCceecCCCCCcCCC
Q psy3500 4 CKTCSTLSRPNISYKYTCYACDYHTLM 30 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~~~~~~ 30 (98)
|+.||.++..... .+.|+.|+..+..
T Consensus 3 C~~Cg~~l~~~~~-~~~C~~C~~~~~~ 28 (104)
T TIGR01384 3 CPKCGSLMTPKNG-VYVCPSCGYEKEK 28 (104)
T ss_pred CcccCcccccCCC-eEECcCCCCcccc
Confidence 8889988866443 5789999866543
No 154
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=75.27 E-value=4.9 Score=16.81 Aligned_cols=21 Identities=33% Similarity=1.031 Sum_probs=14.2
Q ss_pred CCCCCCCCccCCCCCCceecCCCC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
+.|+.|+..+ ....|.|..|.
T Consensus 5 ~~C~~C~~~i---~g~ry~C~~C~ 25 (44)
T smart00291 5 YSCDTCGKPI---VGVRYHCLVCP 25 (44)
T ss_pred cCCCCCCCCC---cCCEEECCCCC
Confidence 5688888732 34577888874
No 155
>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=75.16 E-value=0.94 Score=18.37 Aligned_cols=8 Identities=38% Similarity=1.381 Sum_probs=3.4
Q ss_pred CCCCCCCC
Q psy3500 2 YHCKTCST 9 (98)
Q Consensus 2 ~~c~~c~~ 9 (98)
|+|++||-
T Consensus 7 YkC~~CGn 14 (36)
T PF06397_consen 7 YKCEHCGN 14 (36)
T ss_dssp EE-TTT--
T ss_pred EEccCCCC
Confidence 56777774
No 156
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=75.03 E-value=1.7 Score=22.45 Aligned_cols=14 Identities=21% Similarity=0.408 Sum_probs=7.7
Q ss_pred ecCCCccccccchh
Q psy3500 48 KCEYCAYSCTQSSA 61 (98)
Q Consensus 48 ~c~~c~~~~~~~~~ 61 (98)
.|..|+....-..+
T Consensus 87 ~CM~C~~pLTLd~~ 100 (114)
T PF11023_consen 87 ACMHCKEPLTLDPS 100 (114)
T ss_pred ccCcCCCcCccCch
Confidence 56666655444443
No 157
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=74.97 E-value=2 Score=19.06 Aligned_cols=8 Identities=50% Similarity=1.709 Sum_probs=4.6
Q ss_pred ceecCCCc
Q psy3500 46 PYKCEYCA 53 (98)
Q Consensus 46 ~~~c~~c~ 53 (98)
.|.|+.|+
T Consensus 44 ~y~C~~Cg 51 (54)
T PF10058_consen 44 QYRCPYCG 51 (54)
T ss_pred EEEcCCCC
Confidence 45666655
No 158
>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=74.89 E-value=4.3 Score=23.57 Aligned_cols=27 Identities=22% Similarity=0.269 Sum_probs=20.8
Q ss_pred CCCCceecCCCCCcCCCHHHHHHHHHH
Q psy3500 14 NISYKYTCYACDYHTLMSEDMKKHMRK 40 (98)
Q Consensus 14 ~~~~~~~c~~C~~~~~~~~~l~~h~~~ 40 (98)
..+.+|.|+.|++.|.-..-+..|+..
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhh
Confidence 455679999999999999999999863
No 159
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=74.65 E-value=1.6 Score=22.88 Aligned_cols=12 Identities=25% Similarity=0.944 Sum_probs=7.9
Q ss_pred ceecCCCCCcCCC
Q psy3500 18 KYTCYACDYHTLM 30 (98)
Q Consensus 18 ~~~c~~C~~~~~~ 30 (98)
...| .|+..|..
T Consensus 70 ~~~C-~Cg~~~~~ 81 (124)
T PRK00762 70 EIEC-ECGYEGVV 81 (124)
T ss_pred eEEe-eCcCcccc
Confidence 4678 78766643
No 160
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=74.54 E-value=4 Score=28.12 Aligned_cols=9 Identities=33% Similarity=0.903 Sum_probs=4.0
Q ss_pred ceecCCCcc
Q psy3500 46 PYKCEYCAY 54 (98)
Q Consensus 46 ~~~c~~c~~ 54 (98)
|..|+.||.
T Consensus 475 p~~Cp~Cgs 483 (730)
T COG1198 475 PQSCPECGS 483 (730)
T ss_pred CCCCCCCCC
Confidence 444444443
No 161
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=74.52 E-value=2 Score=17.14 Aligned_cols=23 Identities=26% Similarity=0.680 Sum_probs=8.5
Q ss_pred CCCCCCcc---CCC--CCCceecCCCCC
Q psy3500 4 CKTCSTLS---RPN--ISYKYTCYACDY 26 (98)
Q Consensus 4 c~~c~~~~---~~~--~~~~~~c~~C~~ 26 (98)
|+.||... .+. ....+.|+.|+.
T Consensus 3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred cccccChhhhhcCCCCCccceECCCCCC
Confidence 56666432 232 224566666653
No 162
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=74.29 E-value=2.4 Score=17.60 Aligned_cols=11 Identities=45% Similarity=1.026 Sum_probs=5.5
Q ss_pred CCCCCCCccCC
Q psy3500 3 HCKTCSTLSRP 13 (98)
Q Consensus 3 ~c~~c~~~~~~ 13 (98)
.|++||..+..
T Consensus 15 ~C~~CgM~Y~~ 25 (41)
T PF13878_consen 15 TCPTCGMLYSP 25 (41)
T ss_pred CCCCCCCEECC
Confidence 35555555443
No 163
>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=73.80 E-value=0.65 Score=19.44 Aligned_cols=11 Identities=27% Similarity=0.751 Sum_probs=5.0
Q ss_pred CCCCCCCCCcc
Q psy3500 1 MYHCKTCSTLS 11 (98)
Q Consensus 1 ~~~c~~c~~~~ 11 (98)
||+|+.|+..|
T Consensus 13 ~~~C~~C~~~F 23 (43)
T PF01428_consen 13 PFKCKHCGKSF 23 (43)
T ss_dssp HEE-TTTS-EE
T ss_pred CeECCCCCccc
Confidence 35566666554
No 164
>KOG4167|consensus
Probab=73.75 E-value=0.58 Score=31.77 Aligned_cols=24 Identities=21% Similarity=0.533 Sum_probs=22.0
Q ss_pred eecCCCCCcCCCHHHHHHHHHHhc
Q psy3500 19 YTCYACDYHTLMSEDMKKHMRKHT 42 (98)
Q Consensus 19 ~~c~~C~~~~~~~~~l~~h~~~h~ 42 (98)
|.|.+|++.|.....+..||++|.
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHH
Confidence 899999999988889999999885
No 165
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=73.75 E-value=4.5 Score=16.35 Aligned_cols=9 Identities=33% Similarity=1.073 Sum_probs=4.3
Q ss_pred CCceecCCC
Q psy3500 16 SYKYTCYAC 24 (98)
Q Consensus 16 ~~~~~c~~C 24 (98)
...|.|..|
T Consensus 27 ~qryrC~~C 35 (36)
T PF03811_consen 27 HQRYRCKDC 35 (36)
T ss_pred CEeEecCcC
Confidence 344555544
No 166
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=73.49 E-value=4.9 Score=17.28 Aligned_cols=24 Identities=21% Similarity=0.470 Sum_probs=12.1
Q ss_pred CCCCCCCccCCCCCCceecCCCCC
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACDY 26 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~~ 26 (98)
.|..|++.....+..-|.|..|+.
T Consensus 13 ~C~~C~~~i~g~~~~g~~C~~C~~ 36 (53)
T PF00130_consen 13 YCDVCGKFIWGLGKQGYRCSWCGL 36 (53)
T ss_dssp B-TTSSSBECSSSSCEEEETTTT-
T ss_pred CCcccCcccCCCCCCeEEECCCCC
Confidence 456666655334444566666653
No 167
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.36 E-value=3 Score=21.48 Aligned_cols=14 Identities=21% Similarity=0.323 Sum_probs=8.7
Q ss_pred CCCceecCCCcccc
Q psy3500 43 GEKPYKCEYCAYSC 56 (98)
Q Consensus 43 ~~~~~~c~~c~~~~ 56 (98)
++.|..|++||++|
T Consensus 23 NrdPiVsPytG~s~ 36 (129)
T COG4530 23 NRDPIVSPYTGKSY 36 (129)
T ss_pred CCCccccCcccccc
Confidence 34566666777666
No 168
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=73.23 E-value=3.6 Score=17.96 Aligned_cols=10 Identities=30% Similarity=1.089 Sum_probs=5.6
Q ss_pred ceecCCCccc
Q psy3500 46 PYKCEYCAYS 55 (98)
Q Consensus 46 ~~~c~~c~~~ 55 (98)
.+.|..|+.+
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 3566666643
No 169
>KOG2785|consensus
Probab=72.03 E-value=8.8 Score=24.32 Aligned_cols=26 Identities=35% Similarity=0.507 Sum_probs=21.2
Q ss_pred ceecCCCCCcCCCHHHHHHHHHHhcC
Q psy3500 18 KYTCYACDYHTLMSEDMKKHMRKHTG 43 (98)
Q Consensus 18 ~~~c~~C~~~~~~~~~l~~h~~~h~~ 43 (98)
|-.|..|+..+........||..+.+
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~Hg 191 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHG 191 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccC
Confidence 46689999999998888889976554
No 170
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=71.96 E-value=6 Score=16.58 Aligned_cols=20 Identities=30% Similarity=0.991 Sum_probs=14.2
Q ss_pred CCCCCCCccCCCCCCceecCCCC
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
.|+.|++ +.....|+|..|.
T Consensus 2 ~Cd~C~~---~i~G~ry~C~~C~ 21 (43)
T cd02340 2 ICDGCQG---PIVGVRYKCLVCP 21 (43)
T ss_pred CCCCCCC---cCcCCeEECCCCC
Confidence 4777777 3345688898885
No 171
>PF15269 zf-C2H2_7: Zinc-finger
Probab=71.84 E-value=4.9 Score=17.13 Aligned_cols=23 Identities=26% Similarity=0.717 Sum_probs=18.4
Q ss_pred ceecCCCCCcCCCHHHHHHHHHH
Q psy3500 18 KYTCYACDYHTLMSEDMKKHMRK 40 (98)
Q Consensus 18 ~~~c~~C~~~~~~~~~l~~h~~~ 40 (98)
.|+|-+|..+-..++.|-.||+-
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred cceeecCCcccchHHHHHHHHHH
Confidence 47888888888888888888863
No 172
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=71.58 E-value=4.4 Score=25.52 Aligned_cols=24 Identities=25% Similarity=0.624 Sum_probs=17.2
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
|.|..||..... ...+|+.|+.+-
T Consensus 1 ~~c~~cg~~~~~---~~g~cp~c~~w~ 24 (372)
T cd01121 1 YVCSECGYVSPK---WLGKCPECGEWN 24 (372)
T ss_pred CCCCCCCCCCCC---ccEECcCCCCce
Confidence 789999976543 556788887653
No 173
>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=71.46 E-value=5.2 Score=20.28 Aligned_cols=24 Identities=25% Similarity=0.447 Sum_probs=21.2
Q ss_pred Ceec----CcCcccccChHHHHHHHhhh
Q psy3500 74 PYIC----QQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 74 ~~~C----~~C~~~f~~~~~l~~H~~~h 97 (98)
.|.| ..|+........+..|.+.+
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~ 107 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKE 107 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHh
Confidence 5899 99999999999999998754
No 174
>PRK06450 threonine synthase; Validated
Probab=71.04 E-value=2.6 Score=26.04 Aligned_cols=25 Identities=20% Similarity=0.466 Sum_probs=18.3
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
++|..||+.+.. ...+.|+.|+..+
T Consensus 4 ~~C~~Cg~~~~~--~~~~~C~~cg~~l 28 (338)
T PRK06450 4 EVCMKCGKERES--IYEIRCKKCGGPF 28 (338)
T ss_pred eEECCcCCcCCC--cccccCCcCCCEe
Confidence 579999998854 4457898897543
No 175
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=70.79 E-value=6.2 Score=16.76 Aligned_cols=23 Identities=17% Similarity=0.505 Sum_probs=12.0
Q ss_pred CCCCCCccCCCCCCceecCCCCCcC
Q psy3500 4 CKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
|.+|++ ....+.-..|..|+..|
T Consensus 2 C~vC~~--~~~~~~~i~C~~C~~~~ 24 (51)
T PF00628_consen 2 CPVCGQ--SDDDGDMIQCDSCNRWY 24 (51)
T ss_dssp BTTTTS--SCTTSSEEEBSTTSCEE
T ss_pred CcCCCC--cCCCCCeEEcCCCChhh
Confidence 556666 33333445566666554
No 176
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=70.66 E-value=3.4 Score=26.68 Aligned_cols=25 Identities=24% Similarity=0.608 Sum_probs=17.4
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcCC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHTL 29 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~~ 29 (98)
|.|..||..+.. ...+|+.|+.+-.
T Consensus 8 y~C~~Cg~~~~~---~~g~Cp~C~~w~t 32 (454)
T TIGR00416 8 FVCQHCGADSPK---WQGKCPACHAWNT 32 (454)
T ss_pred EECCcCCCCCcc---ccEECcCCCCccc
Confidence 789999875543 5567888876543
No 177
>PRK12722 transcriptional activator FlhC; Provisional
Probab=70.56 E-value=4 Score=23.17 Aligned_cols=8 Identities=25% Similarity=0.746 Sum_probs=3.7
Q ss_pred CCCCCCcc
Q psy3500 4 CKTCSTLS 11 (98)
Q Consensus 4 c~~c~~~~ 11 (98)
|..||..|
T Consensus 137 C~~Cgg~f 144 (187)
T PRK12722 137 CNCCGGHF 144 (187)
T ss_pred CCCCCCCe
Confidence 44444444
No 178
>KOG2593|consensus
Probab=70.36 E-value=4.8 Score=25.85 Aligned_cols=37 Identities=16% Similarity=0.364 Sum_probs=24.8
Q ss_pred CCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccc
Q psy3500 16 SYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYS 55 (98)
Q Consensus 16 ~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~ 55 (98)
...|.|+.|.+.|.. |...+........|.|..|+..
T Consensus 126 ~~~Y~Cp~C~kkyt~---Lea~~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTS---LEALQLLDNETGEFHCENCGGE 162 (436)
T ss_pred cccccCCccccchhh---hHHHHhhcccCceEEEecCCCc
Confidence 346899999888865 4444444444556889888853
No 179
>PRK11823 DNA repair protein RadA; Provisional
Probab=70.08 E-value=3.6 Score=26.52 Aligned_cols=24 Identities=25% Similarity=0.627 Sum_probs=16.5
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
|.|+.||.... +...+|+.|+.+-
T Consensus 8 y~C~~Cg~~~~---~~~g~Cp~C~~w~ 31 (446)
T PRK11823 8 YVCQECGAESP---KWLGRCPECGAWN 31 (446)
T ss_pred EECCcCCCCCc---ccCeeCcCCCCcc
Confidence 78898886553 3556688887553
No 180
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=70.01 E-value=1.2 Score=20.83 Aligned_cols=26 Identities=19% Similarity=0.522 Sum_probs=15.9
Q ss_pred CCCCCCCC-ccCCCCCCceecCCCCCcCC
Q psy3500 2 YHCKTCST-LSRPNISYKYTCYACDYHTL 29 (98)
Q Consensus 2 ~~c~~c~~-~~~~~~~~~~~c~~C~~~~~ 29 (98)
|.| .||. ++...+.+.-+| .||+...
T Consensus 4 frC-~Cgr~lya~e~~kTkkC-~CG~~l~ 30 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEGAKTKKC-VCGKTLK 30 (68)
T ss_dssp EEE-TTS--EEEETT-SEEEE-TTTEEEE
T ss_pred EEe-cCCCEEEecCCcceeEe-cCCCeee
Confidence 567 4775 455666667778 8887653
No 181
>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=69.71 E-value=5.2 Score=16.40 Aligned_cols=19 Identities=11% Similarity=0.277 Sum_probs=11.4
Q ss_pred CeecCcCcccccChHHHHH
Q psy3500 74 PYICQQCRDTFSSLYLFRN 92 (98)
Q Consensus 74 ~~~C~~C~~~f~~~~~l~~ 92 (98)
.+.|+.|+-.+.....|..
T Consensus 19 id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEECCCCCeEEccHHHHHH
Confidence 3556667666666655543
No 183
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=69.62 E-value=7.7 Score=16.28 Aligned_cols=28 Identities=11% Similarity=0.065 Sum_probs=11.7
Q ss_pred CCCCCCccCCCCCCceecCCCCCcCCCHHH
Q psy3500 4 CKTCSTLSRPNISYKYTCYACDYHTLMSED 33 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~~~~~~~~~ 33 (98)
|++|-+ |......|..-+ ||..|.....
T Consensus 1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl 28 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLP-CGHVFCKDCL 28 (43)
T ss_dssp -TTT-----TTSS-EEE-S-SS-EEEHHHH
T ss_pred CCcccc-ccCCCCCCEEEe-CccHHHHHHH
Confidence 566666 555455555544 7777765443
No 184
>PF04641 Rtf2: Rtf2 RING-finger
Probab=68.77 E-value=5.4 Score=23.73 Aligned_cols=50 Identities=18% Similarity=0.331 Sum_probs=24.3
Q ss_pred CCCCCCCCCccCCCCCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCcccccc
Q psy3500 1 MYHCKTCSTLSRPNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQ 58 (98)
Q Consensus 1 ~~~c~~c~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~ 58 (98)
+|.|++.+.-|......-|- ..||..|..... .. +. ....|++|+..|..
T Consensus 113 ~~~CPvt~~~~~~~~~fv~l-~~cG~V~s~~al-ke-~k-----~~~~Cp~c~~~f~~ 162 (260)
T PF04641_consen 113 RFICPVTGKEFNGKHKFVYL-RPCGCVFSEKAL-KE-LK-----KSKKCPVCGKPFTE 162 (260)
T ss_pred eeECCCCCcccCCceeEEEE-cCCCCEeeHHHH-Hh-hc-----ccccccccCCcccc
Confidence 36666666665322222222 256666654332 21 11 12347788877754
No 185
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=68.56 E-value=4.1 Score=17.24 Aligned_cols=22 Identities=41% Similarity=1.052 Sum_probs=12.8
Q ss_pred CCCCCCCCccCCCCCCceecCCCC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
+.|+.|+.. +.....|.|..|.
T Consensus 5 ~~C~~C~~~--~i~g~Ry~C~~C~ 26 (46)
T PF00569_consen 5 YTCDGCGTD--PIIGVRYHCLVCP 26 (46)
T ss_dssp CE-SSS-SS--SEESSEEEESSSS
T ss_pred eECcCCCCC--cCcCCeEECCCCC
Confidence 567777763 2234678888885
No 186
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=68.40 E-value=3.4 Score=15.95 Aligned_cols=23 Identities=17% Similarity=0.515 Sum_probs=8.8
Q ss_pred CCCCCCc-cCCCCCCceecCCCCC
Q psy3500 4 CKTCSTL-SRPNISYKYTCYACDY 26 (98)
Q Consensus 4 c~~c~~~-~~~~~~~~~~c~~C~~ 26 (98)
|..||.- ....++..-.|+.|+.
T Consensus 6 C~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 6 CGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp -TTT--BEEE-SSSS-EEESSSS-
T ss_pred cCcCCccccCCCCcCEeECCCCcC
Confidence 4455542 2234445556666654
No 187
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=68.39 E-value=4.7 Score=16.87 Aligned_cols=7 Identities=29% Similarity=1.407 Sum_probs=3.2
Q ss_pred eecCCCc
Q psy3500 47 YKCEYCA 53 (98)
Q Consensus 47 ~~c~~c~ 53 (98)
+.|..|+
T Consensus 29 ~~C~~C~ 35 (50)
T cd00029 29 LRCSWCK 35 (50)
T ss_pred eEcCCCC
Confidence 4454443
No 188
>PRK00420 hypothetical protein; Validated
Probab=68.27 E-value=6.6 Score=20.36 Aligned_cols=25 Identities=20% Similarity=0.406 Sum_probs=14.2
Q ss_pred CCCCCCC-ccC-CCCCCceecCCCCCcCC
Q psy3500 3 HCKTCST-LSR-PNISYKYTCYACDYHTL 29 (98)
Q Consensus 3 ~c~~c~~-~~~-~~~~~~~~c~~C~~~~~ 29 (98)
.|+.||. +|. ..+ ...|+.|+....
T Consensus 25 ~CP~Cg~pLf~lk~g--~~~Cp~Cg~~~~ 51 (112)
T PRK00420 25 HCPVCGLPLFELKDG--EVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCcceecCCC--ceECCCCCCeee
Confidence 5777775 344 233 335777776543
No 189
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=67.81 E-value=9.9 Score=17.03 Aligned_cols=31 Identities=13% Similarity=0.203 Sum_probs=13.3
Q ss_pred CceecCCCccccccchhHHHHHHhhCCCCCeecCc
Q psy3500 45 KPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQ 79 (98)
Q Consensus 45 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~ 79 (98)
.|.....|+..|...+- ..++ ...+..+|+.
T Consensus 23 ~PV~s~~C~H~fek~aI-~~~i---~~~~~~~CPv 53 (57)
T PF11789_consen 23 DPVKSKKCGHTFEKEAI-LQYI---QRNGSKRCPV 53 (57)
T ss_dssp SEEEESSS--EEEHHHH-HHHC---TTTS-EE-SC
T ss_pred CCcCcCCCCCeecHHHH-HHHH---HhcCCCCCCC
Confidence 45566666666665543 2232 2233466665
No 190
>PRK12496 hypothetical protein; Provisional
Probab=67.62 E-value=5 Score=22.19 Aligned_cols=12 Identities=17% Similarity=0.468 Sum_probs=7.9
Q ss_pred ceecCCCCCcCC
Q psy3500 18 KYTCYACDYHTL 29 (98)
Q Consensus 18 ~~~c~~C~~~~~ 29 (98)
.|.|.-|++.|.
T Consensus 127 ~~~C~gC~~~~~ 138 (164)
T PRK12496 127 RKVCKGCKKKYP 138 (164)
T ss_pred eEECCCCCcccc
Confidence 466777776663
No 191
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=67.25 E-value=1.5 Score=23.47 Aligned_cols=23 Identities=22% Similarity=0.456 Sum_probs=16.8
Q ss_pred CCCCCCCccCCCCCCceecCCCCCc
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACDYH 27 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~~~ 27 (98)
-|+.||++|...+. ..|+.|.+.
T Consensus 5 nC~~CgklF~~~~~--~iCp~C~~~ 27 (137)
T TIGR03826 5 NCPKCGRLFVKTGR--DVCPSCYEE 27 (137)
T ss_pred cccccchhhhhcCC--ccCHHHhHH
Confidence 48999999998533 358888643
No 192
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=66.43 E-value=4.4 Score=20.12 Aligned_cols=33 Identities=24% Similarity=0.590 Sum_probs=19.2
Q ss_pred ceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccch
Q psy3500 18 KYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSS 60 (98)
Q Consensus 18 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~ 60 (98)
.|.|+.|++.- +. -.+...+.|..|++.|.-..
T Consensus 36 ~y~CpfCgk~~-----vk-----R~a~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 36 KYFCPFCGKHA-----VK-----RQAVGIWRCKGCKKTVAGGA 68 (90)
T ss_pred CccCCCCCCCc-----ee-----eeeeEEEEcCCCCCEEeCCc
Confidence 57788887532 11 11223577888887776543
No 193
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=65.77 E-value=6.9 Score=18.89 Aligned_cols=24 Identities=21% Similarity=0.389 Sum_probs=12.3
Q ss_pred CCCCCCCCccCC-CCCC-ceecCCCC
Q psy3500 2 YHCKTCSTLSRP-NISY-KYTCYACD 25 (98)
Q Consensus 2 ~~c~~c~~~~~~-~~~~-~~~c~~C~ 25 (98)
|.|+.||...-. .++. -..|++|.
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~ 27 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCF 27 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCC
Confidence 578888864332 2221 23466663
No 194
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=65.67 E-value=5.5 Score=16.04 Aligned_cols=22 Identities=23% Similarity=0.431 Sum_probs=8.8
Q ss_pred CCCCCCccCCCCCCceecCCCC
Q psy3500 4 CKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
|..|+..+-.+.+=.|-|..|+
T Consensus 11 C~~C~~~~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 11 CPVCGSRWFYSDDGFYYCDRCG 32 (36)
T ss_pred CCCCCCeEeEccCCEEEhhhCc
Confidence 5555543322222233344443
No 195
>PRK06260 threonine synthase; Validated
Probab=65.62 E-value=4.2 Score=25.67 Aligned_cols=26 Identities=27% Similarity=0.605 Sum_probs=19.5
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
++|..||+.+... ...+.|+.|+..+
T Consensus 4 ~~C~~cg~~~~~~-~~~~~Cp~cg~~l 29 (397)
T PRK06260 4 LKCIECGKEYDPD-EIIYTCPECGGLL 29 (397)
T ss_pred EEECCCCCCCCCC-CccccCCCCCCeE
Confidence 5799999998754 4468899997543
No 196
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=65.55 E-value=6 Score=15.68 Aligned_cols=11 Identities=18% Similarity=0.597 Sum_probs=6.0
Q ss_pred eecCcCccccc
Q psy3500 75 YICQQCRDTFS 85 (98)
Q Consensus 75 ~~C~~C~~~f~ 85 (98)
+.|+.|++...
T Consensus 5 ~~C~nC~R~v~ 15 (33)
T PF08209_consen 5 VECPNCGRPVA 15 (33)
T ss_dssp EE-TTTSSEEE
T ss_pred EECCCCcCCcc
Confidence 56667766543
No 197
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=65.33 E-value=2.7 Score=16.53 Aligned_cols=9 Identities=33% Similarity=1.320 Sum_probs=5.7
Q ss_pred CCCCCCCCc
Q psy3500 2 YHCKTCSTL 10 (98)
Q Consensus 2 ~~c~~c~~~ 10 (98)
|+|+.||..
T Consensus 5 ykC~~CGni 13 (34)
T cd00974 5 YKCEICGNI 13 (34)
T ss_pred EEcCCCCcE
Confidence 567777753
No 198
>PRK11032 hypothetical protein; Provisional
Probab=65.27 E-value=5.1 Score=22.15 Aligned_cols=8 Identities=25% Similarity=0.754 Sum_probs=4.1
Q ss_pred eecCCCCC
Q psy3500 19 YTCYACDY 26 (98)
Q Consensus 19 ~~c~~C~~ 26 (98)
..|..||.
T Consensus 125 LvC~~Cg~ 132 (160)
T PRK11032 125 LVCEKCHH 132 (160)
T ss_pred EEecCCCC
Confidence 44555554
No 199
>KOG2907|consensus
Probab=65.24 E-value=4.3 Score=21.02 Aligned_cols=38 Identities=24% Similarity=0.592 Sum_probs=18.7
Q ss_pred eecCCCccccccchhHHHHHHhhCCCC-CeecCcCccccc
Q psy3500 47 YKCEYCAYSCTQSSALKIHERKHTGDK-PYICQQCRDTFS 85 (98)
Q Consensus 47 ~~c~~c~~~~~~~~~l~~h~~~~~~~~-~~~C~~C~~~f~ 85 (98)
..|+.||..-..-..++-+ ...-|.- =|.|+.|+..|.
T Consensus 75 ~kCpkCghe~m~Y~T~QlR-SADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQLR-SADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred ccCcccCCchhhhhhhhcc-cccCCceEEEEcCccceeee
Confidence 5688887532222222111 1122332 277888877664
No 200
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=65.17 E-value=19 Score=22.30 Aligned_cols=53 Identities=19% Similarity=0.206 Sum_probs=29.4
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccc
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQS 59 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~ 59 (98)
+.|+.|....-.+....+--..||..|-.... .... ...+..|+.|+..+...
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv-~~l~----~~~~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCV-DLLF----VRGSGSCPECDTPLRKN 56 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHH-HHHh----cCCCCCCCCCCCccchh
Confidence 57888887533333322222378888865432 3221 12345799998765544
No 201
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=64.51 E-value=5.8 Score=15.66 Aligned_cols=11 Identities=18% Similarity=0.334 Sum_probs=6.0
Q ss_pred ceecCCCCCcC
Q psy3500 18 KYTCYACDYHT 28 (98)
Q Consensus 18 ~~~c~~C~~~~ 28 (98)
-+.|..|+..|
T Consensus 21 ~~~C~~Cg~~~ 31 (33)
T PF08792_consen 21 YEVCIFCGSSF 31 (33)
T ss_pred eEEcccCCcEe
Confidence 34566666544
No 202
>PRK12860 transcriptional activator FlhC; Provisional
Probab=64.50 E-value=5.8 Score=22.58 Aligned_cols=8 Identities=25% Similarity=1.020 Sum_probs=3.8
Q ss_pred ceecCCCc
Q psy3500 46 PYKCEYCA 53 (98)
Q Consensus 46 ~~~c~~c~ 53 (98)
.|.|+.|.
T Consensus 154 ~f~CplC~ 161 (189)
T PRK12860 154 NFVCGLCQ 161 (189)
T ss_pred CCcCCCCC
Confidence 34455544
No 203
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=64.15 E-value=6.8 Score=22.33 Aligned_cols=26 Identities=27% Similarity=0.540 Sum_probs=18.8
Q ss_pred CCCCCCCCCccCCCCCCceec-CCCCC
Q psy3500 1 MYHCKTCSTLSRPNISYKYTC-YACDY 26 (98)
Q Consensus 1 ~~~c~~c~~~~~~~~~~~~~c-~~C~~ 26 (98)
|-+|++||.-|.+.......| +.|+.
T Consensus 6 ~rKCKvCg~~F~P~~s~q~vCSpeCa~ 32 (189)
T PF05766_consen 6 RRKCKVCGEWFVPARSNQKVCSPECAI 32 (189)
T ss_pred CCcCcccCCccccCCCceeeeCHHHHh
Confidence 357999999999866655554 46663
No 204
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=64.07 E-value=7.8 Score=15.99 Aligned_cols=8 Identities=25% Similarity=0.675 Sum_probs=3.5
Q ss_pred CCCCCCcc
Q psy3500 4 CKTCSTLS 11 (98)
Q Consensus 4 c~~c~~~~ 11 (98)
|..|++.+
T Consensus 14 C~~C~~~i 21 (49)
T smart00109 14 CCVCRKSI 21 (49)
T ss_pred cccccccc
Confidence 44444433
No 205
>PRK07591 threonine synthase; Validated
Probab=63.97 E-value=4.8 Score=25.72 Aligned_cols=25 Identities=16% Similarity=0.356 Sum_probs=18.8
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
++|..||+.+... .. +.|+.|+..+
T Consensus 19 l~C~~Cg~~~~~~-~~-~~C~~cg~~l 43 (421)
T PRK07591 19 LKCRECGAEYPLG-PI-HVCEECFGPL 43 (421)
T ss_pred EEeCCCCCcCCCC-CC-ccCCCCCCeE
Confidence 4788999988765 34 8899897543
No 206
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=63.78 E-value=7.5 Score=15.92 Aligned_cols=24 Identities=17% Similarity=0.571 Sum_probs=9.2
Q ss_pred CCCCCCCccC-----CCCCCceecCCCCC
Q psy3500 3 HCKTCSTLSR-----PNISYKYTCYACDY 26 (98)
Q Consensus 3 ~c~~c~~~~~-----~~~~~~~~c~~C~~ 26 (98)
.|+.|+.-.. ..+.+.+.|..|+.
T Consensus 4 rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp B-TTT--BS-TTSEEETTTTEEEETTT--
T ss_pred ccCCCCCEECCcceEcCCCCEEECcCCCC
Confidence 4566664332 12334566666654
No 207
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=63.62 E-value=2.9 Score=16.41 Aligned_cols=9 Identities=33% Similarity=1.342 Sum_probs=5.5
Q ss_pred CCCCCCCCc
Q psy3500 2 YHCKTCSTL 10 (98)
Q Consensus 2 ~~c~~c~~~ 10 (98)
|+|+.||..
T Consensus 8 ykC~~Cgni 16 (34)
T TIGR00319 8 YKCEVCGNI 16 (34)
T ss_pred EEcCCCCcE
Confidence 566666653
No 208
>PRK08329 threonine synthase; Validated
Probab=63.47 E-value=7.9 Score=24.04 Aligned_cols=25 Identities=24% Similarity=0.643 Sum_probs=18.3
Q ss_pred CCCCCCCCCccCCCCCCceecCCCCCcC
Q psy3500 1 MYHCKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 1 ~~~c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
+++|..||+.+.. . ..+.| .|+-.+
T Consensus 1 ~l~C~~Cg~~~~~-~-~~~~C-~c~~~l 25 (347)
T PRK08329 1 MLRCTKCGRTYEE-K-FKLRC-DCGGTL 25 (347)
T ss_pred CcCcCCCCCCcCC-C-Cceec-CCCCcE
Confidence 5789999999963 3 34889 686543
No 209
>PHA02942 putative transposase; Provisional
Probab=63.29 E-value=20 Score=22.82 Aligned_cols=13 Identities=23% Similarity=0.805 Sum_probs=7.2
Q ss_pred ceecCCCcccccc
Q psy3500 46 PYKCEYCAYSCTQ 58 (98)
Q Consensus 46 ~~~c~~c~~~~~~ 58 (98)
.|.|+.||.....
T Consensus 342 ~f~C~~CG~~~dr 354 (383)
T PHA02942 342 YFHCPSCGYENDR 354 (383)
T ss_pred EEECCCCCCEeCc
Confidence 4666666654433
No 210
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=63.05 E-value=3.9 Score=17.82 Aligned_cols=16 Identities=31% Similarity=0.694 Sum_probs=11.6
Q ss_pred CCCeecCcCcccccCh
Q psy3500 72 DKPYICQQCRDTFSSL 87 (98)
Q Consensus 72 ~~~~~C~~C~~~f~~~ 87 (98)
++.+.|..||..|...
T Consensus 2 Dk~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFT 17 (49)
T ss_pred CeeEEcccCCCeEEEe
Confidence 4567888888877643
No 211
>KOG2906|consensus
Probab=63.02 E-value=0.25 Score=24.69 Aligned_cols=30 Identities=23% Similarity=0.612 Sum_probs=19.2
Q ss_pred CCCCCCCCccC-CCCC--CceecCCCCCcCCCH
Q psy3500 2 YHCKTCSTLSR-PNIS--YKYTCYACDYHTLMS 31 (98)
Q Consensus 2 ~~c~~c~~~~~-~~~~--~~~~c~~C~~~~~~~ 31 (98)
.=|+.||-+.. ..++ ..|.|+.|+..+...
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcCCCCceeeEe
Confidence 34888886443 3333 357888888777554
No 212
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=62.38 E-value=9.8 Score=22.73 Aligned_cols=11 Identities=36% Similarity=1.198 Sum_probs=7.1
Q ss_pred eecCcCccccc
Q psy3500 75 YICQQCRDTFS 85 (98)
Q Consensus 75 ~~C~~C~~~f~ 85 (98)
|.|+.|+..|.
T Consensus 156 f~C~~C~h~F~ 166 (278)
T PF15135_consen 156 FHCPKCRHNFR 166 (278)
T ss_pred eecccccccch
Confidence 66666666664
No 213
>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=62.34 E-value=5.7 Score=20.22 Aligned_cols=7 Identities=43% Similarity=1.587 Sum_probs=3.9
Q ss_pred eecCcCc
Q psy3500 75 YICQQCR 81 (98)
Q Consensus 75 ~~C~~C~ 81 (98)
|.|..|+
T Consensus 32 y~C~~C~ 38 (102)
T PF11672_consen 32 YVCTPCD 38 (102)
T ss_pred EECCCCC
Confidence 5565554
No 214
>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=62.25 E-value=4.6 Score=17.22 Aligned_cols=6 Identities=33% Similarity=1.331 Sum_probs=3.3
Q ss_pred CCCCCC
Q psy3500 4 CKTCST 9 (98)
Q Consensus 4 c~~c~~ 9 (98)
|+.||.
T Consensus 2 CP~Cg~ 7 (47)
T PF04606_consen 2 CPHCGS 7 (47)
T ss_pred cCCCCC
Confidence 555653
No 215
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=61.89 E-value=7.4 Score=16.29 Aligned_cols=10 Identities=20% Similarity=0.624 Sum_probs=6.2
Q ss_pred CCCCCCCccC
Q psy3500 3 HCKTCSTLSR 12 (98)
Q Consensus 3 ~c~~c~~~~~ 12 (98)
.|+.||..+.
T Consensus 4 ~C~~Cg~~l~ 13 (47)
T PF13005_consen 4 ACPDCGGELK 13 (47)
T ss_pred cCCCCCceee
Confidence 4677776544
No 216
>PHA02998 RNA polymerase subunit; Provisional
Probab=61.32 E-value=1.9 Score=24.18 Aligned_cols=42 Identities=14% Similarity=0.331 Sum_probs=21.7
Q ss_pred ceecCCCccccccchhHHHHHHhhCCCCCeecCcCcccccCh
Q psy3500 46 PYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFSSL 87 (98)
Q Consensus 46 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 87 (98)
...|+.|+..-.....++.+..-.....=|.|..||..|..+
T Consensus 143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCCc
Confidence 356888875433333222221111112237898998877654
No 217
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=60.23 E-value=15 Score=16.20 Aligned_cols=45 Identities=7% Similarity=-0.003 Sum_probs=26.1
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccc
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCT 57 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~ 57 (98)
|.|.+|+..++.. . ...||..|.... +...... ...|+.|+..+.
T Consensus 2 ~~Cpi~~~~~~~P----v-~~~~G~v~~~~~-i~~~~~~-----~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKDP----V-ILPSGQTYERRA-IEKWLLS-----HGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCCC----E-ECCCCCEEeHHH-HHHHHHH-----CCCCCCCcCCCC
Confidence 5688888887652 2 235676665433 3333332 236788776653
No 218
>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=58.42 E-value=2.8 Score=18.46 Aligned_cols=17 Identities=18% Similarity=0.495 Sum_probs=6.2
Q ss_pred CceecCCCccccccchh
Q psy3500 45 KPYKCEYCAYSCTQSSA 61 (98)
Q Consensus 45 ~~~~c~~c~~~~~~~~~ 61 (98)
..|.|+.|...|-..=.
T Consensus 20 ~~y~C~~C~~~FC~dCD 36 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCD 36 (51)
T ss_dssp EEE--TTTT--B-HHHH
T ss_pred CeEECCCCCCccccCcC
Confidence 34566666655554433
No 219
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=58.40 E-value=3.6 Score=19.30 Aligned_cols=31 Identities=23% Similarity=0.459 Sum_probs=16.8
Q ss_pred ceecCCCccccccchhHHHHHHhhCCCCCeecCcCcccc
Q psy3500 46 PYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTF 84 (98)
Q Consensus 46 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 84 (98)
...|..|+..+..... ..+ ..+.|+.|+..|
T Consensus 41 ~v~Cg~C~~~~~~~~~-------~c~-~~~~C~~C~~~~ 71 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEY-------SCG-ADYFCPICGLYF 71 (71)
T ss_dssp EEEETTT--EEES-SB-------TT---SEEETTTTEEE
T ss_pred CeECCCCCCccChhhh-------hcC-CCccCcCcCCCC
Confidence 5778888876665543 111 358888887543
No 220
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=57.52 E-value=6.6 Score=17.60 Aligned_cols=7 Identities=29% Similarity=1.345 Sum_probs=3.1
Q ss_pred CCCCCCC
Q psy3500 2 YHCKTCS 8 (98)
Q Consensus 2 ~~c~~c~ 8 (98)
|+|+.||
T Consensus 15 ~~Cp~cG 21 (55)
T PF13824_consen 15 FECPDCG 21 (55)
T ss_pred CcCCCCC
Confidence 3444444
No 221
>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=57.35 E-value=3.2 Score=15.81 Aligned_cols=9 Identities=22% Similarity=0.604 Sum_probs=4.8
Q ss_pred ecCCCcccc
Q psy3500 48 KCEYCAYSC 56 (98)
Q Consensus 48 ~c~~c~~~~ 56 (98)
.|..|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 455555555
No 222
>KOG2231|consensus
Probab=57.10 E-value=30 Score=23.93 Aligned_cols=45 Identities=24% Similarity=0.470 Sum_probs=25.9
Q ss_pred ecCCCCCcCCCHHHHHHHHHHhcCCCceecCCC------ccccccchhHHHHHHh
Q psy3500 20 TCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYC------AYSCTQSSALKIHERK 68 (98)
Q Consensus 20 ~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c------~~~~~~~~~l~~h~~~ 68 (98)
.|..|...|.....|..|++.+. +.|..| +..|..-..|..|.+.
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~ 234 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRK 234 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhh
Confidence 46677777777777776665432 334444 2344555666666553
No 223
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=57.06 E-value=8.8 Score=17.41 Aligned_cols=32 Identities=25% Similarity=0.585 Sum_probs=19.7
Q ss_pred ceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccc
Q psy3500 18 KYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYS 55 (98)
Q Consensus 18 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~ 55 (98)
.|.|+ ||-+|..+ |.. ...|+.-..|+-|...
T Consensus 22 tyPCP-CGDRFeIs--LeD---l~~GE~VArCPSCSLi 53 (67)
T COG5216 22 TYPCP-CGDRFEIS--LED---LRNGEVVARCPSCSLI 53 (67)
T ss_pred EecCC-CCCEeEEE--HHH---hhCCceEEEcCCceEE
Confidence 46674 88777543 221 2357777888888743
No 224
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=56.92 E-value=2.3 Score=21.24 Aligned_cols=21 Identities=24% Similarity=0.591 Sum_probs=12.1
Q ss_pred CCCCCCCCc--------cCCCCCCceecC
Q psy3500 2 YHCKTCSTL--------SRPNISYKYTCY 22 (98)
Q Consensus 2 ~~c~~c~~~--------~~~~~~~~~~c~ 22 (98)
|+|-+||.. |...|...|.|-
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl 35 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECL 35 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHH
Confidence 567777753 344555556553
No 225
>KOG2482|consensus
Probab=56.76 E-value=7.3 Score=24.40 Aligned_cols=23 Identities=17% Similarity=0.511 Sum_probs=20.8
Q ss_pred CeecCcCcccccChHHHHHHHhh
Q psy3500 74 PYICQQCRDTFSSLYLFRNHLQS 96 (98)
Q Consensus 74 ~~~C~~C~~~f~~~~~l~~H~~~ 96 (98)
.+.|..|.+.|..+..|..|||.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 47899999999999999999974
No 226
>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=56.71 E-value=6.6 Score=19.55 Aligned_cols=33 Identities=24% Similarity=0.554 Sum_probs=18.6
Q ss_pred ceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccch
Q psy3500 18 KYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSS 60 (98)
Q Consensus 18 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~ 60 (98)
.|.|+.|++.- +. -.+-..+.|..|++.|.-..
T Consensus 35 ~y~CpfCgk~~-----vk-----R~a~GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 35 KYVCPFCGKKT-----VK-----RGSTGIWTCRKCGAKFAGGA 67 (91)
T ss_pred CccCCCCCCCc-----eE-----EEeeEEEEcCCCCCEEeCCc
Confidence 57788887432 11 11223477888887766543
No 227
>PLN02294 cytochrome c oxidase subunit Vb
Probab=56.51 E-value=7.7 Score=21.72 Aligned_cols=19 Identities=26% Similarity=0.608 Sum_probs=13.9
Q ss_pred HhhCCCCCeecCcCcccccC
Q psy3500 67 RKHTGDKPYICQQCRDTFSS 86 (98)
Q Consensus 67 ~~~~~~~~~~C~~C~~~f~~ 86 (98)
..+.| +|.+|++||..|..
T Consensus 135 ~L~kG-kp~RCpeCG~~fkL 153 (174)
T PLN02294 135 WLEKG-KSFECPVCTQYFEL 153 (174)
T ss_pred EecCC-CceeCCCCCCEEEE
Confidence 34444 58999999988764
No 228
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.45 E-value=6.2 Score=20.76 Aligned_cols=26 Identities=27% Similarity=0.554 Sum_probs=12.2
Q ss_pred CCCCCCC--ccCCCCCCceecCCCCCcC
Q psy3500 3 HCKTCST--LSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 3 ~c~~c~~--~~~~~~~~~~~c~~C~~~~ 28 (98)
.|+.||+ +|+-=.+..-.|..||..+
T Consensus 23 rCP~CGeGrLF~gFLK~~p~C~aCG~dy 50 (126)
T COG5349 23 RCPRCGEGRLFRGFLKVVPACEACGLDY 50 (126)
T ss_pred CCCCCCCchhhhhhcccCchhhhccccc
Confidence 3666664 3332223334466665443
No 229
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=56.42 E-value=7.7 Score=25.09 Aligned_cols=23 Identities=26% Similarity=0.677 Sum_probs=15.0
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCc
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYH 27 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~ 27 (98)
|.|+.||-... +..-+|+.|+.+
T Consensus 8 f~C~~CG~~s~---KW~GkCp~Cg~W 30 (456)
T COG1066 8 FVCQECGYVSP---KWLGKCPACGAW 30 (456)
T ss_pred EEcccCCCCCc---cccccCCCCCCc
Confidence 78888886543 344567777754
No 230
>PRK04351 hypothetical protein; Provisional
Probab=56.33 E-value=8.7 Score=20.96 Aligned_cols=34 Identities=26% Similarity=0.597 Sum_probs=21.7
Q ss_pred CceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCcccccc
Q psy3500 17 YKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQ 58 (98)
Q Consensus 17 ~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~ 58 (98)
..|.|..|+..+.. ++ .+ ....+.|..|+..+..
T Consensus 111 y~Y~C~~Cg~~~~r------~R-r~-n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 111 YLYECQSCGQQYLR------KR-RI-NTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEEECCCCCCEeee------ee-ec-CCCcEEeCCCCcEeee
Confidence 45889889866532 11 22 2356899999876554
No 231
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=55.87 E-value=4.7 Score=19.53 Aligned_cols=14 Identities=21% Similarity=0.456 Sum_probs=8.0
Q ss_pred ceecCCCccccccc
Q psy3500 46 PYKCEYCAYSCTQS 59 (98)
Q Consensus 46 ~~~c~~c~~~~~~~ 59 (98)
...|..|+..|...
T Consensus 46 ~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 46 ILSCRVCGESFQTK 59 (81)
T ss_dssp EEEESSS--EEEEE
T ss_pred EEEecCCCCeEEEc
Confidence 36788888766554
No 232
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=55.08 E-value=13 Score=16.68 Aligned_cols=8 Identities=25% Similarity=0.658 Sum_probs=4.4
Q ss_pred eecCCCCC
Q psy3500 19 YTCYACDY 26 (98)
Q Consensus 19 ~~c~~C~~ 26 (98)
..|+.||.
T Consensus 28 ~~C~~CG~ 35 (57)
T PRK12286 28 VECPNCGE 35 (57)
T ss_pred eECCCCCC
Confidence 34666654
No 233
>PF03563 Bunya_G2: Bunyavirus glycoprotein G2; InterPro: IPR005168 Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This entry represents the polyprotein region forming the G2 glycoprotein, which interacts with the IPR005167 from INTERPRO G1 glycoprotein [].
Probab=55.04 E-value=19 Score=21.83 Aligned_cols=16 Identities=31% Similarity=0.449 Sum_probs=9.2
Q ss_pred CCCCcCCCHHHHHHHH
Q psy3500 23 ACDYHTLMSEDMKKHM 38 (98)
Q Consensus 23 ~C~~~~~~~~~l~~h~ 38 (98)
+||..|...+.|+.|+
T Consensus 255 vCG~~f~~sd~mk~HR 270 (285)
T PF03563_consen 255 VCGMKFETSDRMKMHR 270 (285)
T ss_pred eccccccchHHHHHHH
Confidence 4566666655555554
No 234
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=54.55 E-value=5 Score=23.05 Aligned_cols=17 Identities=12% Similarity=0.221 Sum_probs=11.8
Q ss_pred CCCCceecCCCCCcCCC
Q psy3500 14 NISYKYTCYACDYHTLM 30 (98)
Q Consensus 14 ~~~~~~~c~~C~~~~~~ 30 (98)
..++||.|.+|-+.|..
T Consensus 192 ~e~IPF~C~iCKkdy~s 208 (259)
T COG5152 192 GEKIPFLCGICKKDYES 208 (259)
T ss_pred CCCCceeehhchhhccc
Confidence 34568888888777654
No 235
>PF15616 TerY-C: TerY-C metal binding domain
Probab=54.51 E-value=8.7 Score=20.54 Aligned_cols=13 Identities=23% Similarity=0.250 Sum_probs=6.8
Q ss_pred CCCceecCCCCCc
Q psy3500 15 ISYKYTCYACDYH 27 (98)
Q Consensus 15 ~~~~~~c~~C~~~ 27 (98)
++....|+.|++.
T Consensus 102 g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 102 GEGEVTCPWCGNE 114 (131)
T ss_pred CCCCEECCCCCCe
Confidence 3445556666544
No 236
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=54.31 E-value=13 Score=16.59 Aligned_cols=8 Identities=25% Similarity=0.663 Sum_probs=4.4
Q ss_pred eecCCCCC
Q psy3500 19 YTCYACDY 26 (98)
Q Consensus 19 ~~c~~C~~ 26 (98)
-.|+.||.
T Consensus 27 ~~C~~cG~ 34 (55)
T TIGR01031 27 VVCPNCGE 34 (55)
T ss_pred eECCCCCC
Confidence 34666654
No 237
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=54.19 E-value=5.5 Score=17.29 Aligned_cols=8 Identities=25% Similarity=0.987 Sum_probs=3.0
Q ss_pred eecCcCcc
Q psy3500 75 YICQQCRD 82 (98)
Q Consensus 75 ~~C~~C~~ 82 (98)
|.|+.|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 77777764
No 238
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=53.30 E-value=8.8 Score=24.44 Aligned_cols=22 Identities=18% Similarity=0.413 Sum_probs=16.8
Q ss_pred CCCCCCCCccCCCCCCceecCCCC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
++|..||+.+. ....+.|+.|+
T Consensus 3 l~C~~Cg~~~~--~~~~~~C~~c~ 24 (398)
T TIGR03844 3 LRCPGCGEVLP--DHYTLSCPLDC 24 (398)
T ss_pred EEeCCCCCccC--CccccCCCCCC
Confidence 57999999985 33468898776
No 239
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=52.95 E-value=32 Score=19.49 Aligned_cols=33 Identities=18% Similarity=0.581 Sum_probs=20.7
Q ss_pred CCCceecCCCccccccchhHHHHHHhhCCCCCeecCcCcccc
Q psy3500 43 GEKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTF 84 (98)
Q Consensus 43 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 84 (98)
...-|.|+.|...++...+. .. .|.|+.||...
T Consensus 110 ~~~~y~C~~~~~r~sfdeA~------~~---~F~Cp~Cg~~L 142 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEAM------EL---GFTCPKCGEDL 142 (176)
T ss_pred cCCceeCCCCCCcccHHHHH------Hh---CCCCCCCCchh
Confidence 34458888777666554432 22 28899998653
No 240
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=52.33 E-value=8.2 Score=14.53 Aligned_cols=18 Identities=22% Similarity=0.593 Sum_probs=6.9
Q ss_pred CCCCCCc-cCCCCCCceec
Q psy3500 4 CKTCSTL-SRPNISYKYTC 21 (98)
Q Consensus 4 c~~c~~~-~~~~~~~~~~c 21 (98)
|+.||.. .+..++..+.|
T Consensus 2 CP~C~s~l~~~~~ev~~~C 20 (28)
T PF03119_consen 2 CPVCGSKLVREEGEVDIRC 20 (28)
T ss_dssp -TTT--BEEE-CCTTCEEE
T ss_pred cCCCCCEeEcCCCCEeEEC
Confidence 6666643 33444444444
No 241
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=52.30 E-value=13 Score=17.13 Aligned_cols=9 Identities=33% Similarity=0.862 Sum_probs=5.2
Q ss_pred CCCCCCCcc
Q psy3500 3 HCKTCSTLS 11 (98)
Q Consensus 3 ~c~~c~~~~ 11 (98)
.|++||+..
T Consensus 8 ~CP~C~k~~ 16 (62)
T PRK00418 8 NCPTCGKPV 16 (62)
T ss_pred cCCCCCCcc
Confidence 466666654
No 242
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=51.30 E-value=18 Score=15.83 Aligned_cols=13 Identities=31% Similarity=0.700 Sum_probs=7.1
Q ss_pred eecCCCccccccc
Q psy3500 47 YKCEYCAYSCTQS 59 (98)
Q Consensus 47 ~~c~~c~~~~~~~ 59 (98)
+.|+.|+..+...
T Consensus 29 W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKCPKCGHEWKAS 41 (55)
T ss_pred EECCCCCCeeEcc
Confidence 5566665554443
No 243
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.16 E-value=26 Score=21.18 Aligned_cols=15 Identities=20% Similarity=0.771 Sum_probs=8.4
Q ss_pred CceecCCCccccccc
Q psy3500 45 KPYKCEYCAYSCTQS 59 (98)
Q Consensus 45 ~~~~c~~c~~~~~~~ 59 (98)
+.+.|+.||......
T Consensus 321 r~~~C~~cg~~~~rD 335 (364)
T COG0675 321 RLFKCPRCGFVHDRD 335 (364)
T ss_pred eeEECCCCCCeehhh
Confidence 346666666554444
No 244
>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=49.80 E-value=11 Score=19.05 Aligned_cols=19 Identities=32% Similarity=0.678 Sum_probs=14.1
Q ss_pred HhhCCCCCeecCcCcccccC
Q psy3500 67 RKHTGDKPYICQQCRDTFSS 86 (98)
Q Consensus 67 ~~~~~~~~~~C~~C~~~f~~ 86 (98)
..+.+ ++.+|.+||.-|..
T Consensus 73 ~l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 73 WLEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EEeCC-CceeCCCCCcEEEE
Confidence 34555 68999999987753
No 245
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=49.79 E-value=13 Score=25.23 Aligned_cols=19 Identities=32% Similarity=0.669 Sum_probs=9.8
Q ss_pred CCCCCCccCCCCCCceecCCCCC
Q psy3500 4 CKTCSTLSRPNISYKYTCYACDY 26 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~~ 26 (98)
|..||. .++..+.|+.||.
T Consensus 562 C~~CGy----~g~~~~~CP~CG~ 580 (618)
T PRK14704 562 CKCCSY----HGVIGNECPSCGN 580 (618)
T ss_pred cCCCCC----CCCcCccCcCCCC
Confidence 555553 2333456666664
No 246
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=49.70 E-value=15 Score=16.71 Aligned_cols=26 Identities=27% Similarity=0.636 Sum_probs=13.0
Q ss_pred CCCCCCC-----ccCCCCCCceecCCCCCcC
Q psy3500 3 HCKTCST-----LSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 3 ~c~~c~~-----~~~~~~~~~~~c~~C~~~~ 28 (98)
+|+.|+. ++...+...-+|-.||..-
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 3555554 2334444445566666543
No 247
>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=49.63 E-value=7.5 Score=17.00 Aligned_cols=13 Identities=15% Similarity=0.488 Sum_probs=7.2
Q ss_pred ecCCCccccccch
Q psy3500 48 KCEYCAYSCTQSS 60 (98)
Q Consensus 48 ~c~~c~~~~~~~~ 60 (98)
.||+|++.|....
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 8999999887653
No 248
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=49.50 E-value=33 Score=17.01 Aligned_cols=12 Identities=17% Similarity=0.260 Sum_probs=5.7
Q ss_pred eecCCCCCcCCC
Q psy3500 19 YTCYACDYHTLM 30 (98)
Q Consensus 19 ~~c~~C~~~~~~ 30 (98)
-.|+.|+....-
T Consensus 34 S~C~~C~~~L~~ 45 (92)
T PF06750_consen 34 SHCPHCGHPLSW 45 (92)
T ss_pred CcCcCCCCcCcc
Confidence 345555544433
No 249
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=49.36 E-value=9.5 Score=16.25 Aligned_cols=11 Identities=45% Similarity=0.993 Sum_probs=7.4
Q ss_pred CCCCCCCCccC
Q psy3500 2 YHCKTCSTLSR 12 (98)
Q Consensus 2 ~~c~~c~~~~~ 12 (98)
|.|++||....
T Consensus 1 y~C~~Cg~D~t 11 (45)
T cd02336 1 YHCFTCGNDCT 11 (45)
T ss_pred CcccCCCCccC
Confidence 57888886543
No 250
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=48.74 E-value=10 Score=18.88 Aligned_cols=33 Identities=21% Similarity=0.526 Sum_probs=18.5
Q ss_pred ceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccccch
Q psy3500 18 KYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQSS 60 (98)
Q Consensus 18 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~ 60 (98)
.|.|+.|++.-. . -.+-..+.|..|++.|.-..
T Consensus 36 ~y~CpfCgk~~v-----k-----R~a~GIW~C~~C~~~~AGGA 68 (90)
T PRK03976 36 KHVCPVCGRPKV-----K-----RVGTGIWECRKCGAKFAGGA 68 (90)
T ss_pred CccCCCCCCCce-----E-----EEEEEEEEcCCCCCEEeCCc
Confidence 577888864321 1 11223477888887766543
No 252
>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=48.66 E-value=24 Score=23.36 Aligned_cols=7 Identities=29% Similarity=0.880 Sum_probs=2.9
Q ss_pred eecCCCC
Q psy3500 19 YTCYACD 25 (98)
Q Consensus 19 ~~c~~C~ 25 (98)
..|..||
T Consensus 241 l~Ch~Cg 247 (505)
T TIGR00595 241 LRCHYCG 247 (505)
T ss_pred EEcCCCc
Confidence 3444443
No 253
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=48.59 E-value=5.9 Score=20.50 Aligned_cols=28 Identities=32% Similarity=0.685 Sum_probs=18.2
Q ss_pred CCCCCCccCCC---CCCceecCCCCCcCCCH
Q psy3500 4 CKTCSTLSRPN---ISYKYTCYACDYHTLMS 31 (98)
Q Consensus 4 c~~c~~~~~~~---~~~~~~c~~C~~~~~~~ 31 (98)
|+.||.+..+. ++-.+.|..||......
T Consensus 5 Cp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 5 CPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred cCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 77888766542 33378888888665443
No 254
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.07 E-value=4.8 Score=19.31 Aligned_cols=32 Identities=28% Similarity=0.660 Sum_probs=17.9
Q ss_pred CceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccc
Q psy3500 17 YKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYS 55 (98)
Q Consensus 17 ~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~ 55 (98)
..|+|.+|+..| .+..+|. ..-.-.|+.|+..
T Consensus 11 Y~Y~c~~cg~~~----dvvq~~~---ddplt~ce~c~a~ 42 (82)
T COG2331 11 YSYECTECGNRF----DVVQAMT---DDPLTTCEECGAR 42 (82)
T ss_pred eEEeecccchHH----HHHHhcc---cCccccChhhChH
Confidence 458888888766 3333332 1112357777753
No 255
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.94 E-value=10 Score=17.54 Aligned_cols=10 Identities=30% Similarity=0.634 Sum_probs=6.9
Q ss_pred CCCCCCCccC
Q psy3500 3 HCKTCSTLSR 12 (98)
Q Consensus 3 ~c~~c~~~~~ 12 (98)
+|++||+--.
T Consensus 9 ~CP~Cgkpv~ 18 (65)
T COG3024 9 PCPTCGKPVV 18 (65)
T ss_pred cCCCCCCccc
Confidence 5788887544
No 256
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=47.74 E-value=12 Score=14.05 Aligned_cols=23 Identities=26% Similarity=0.580 Sum_probs=9.3
Q ss_pred CCCCCCCccC---CCCCCceecCCCC
Q psy3500 3 HCKTCSTLSR---PNISYKYTCYACD 25 (98)
Q Consensus 3 ~c~~c~~~~~---~~~~~~~~c~~C~ 25 (98)
+|+.|+.-+. ..+...+-|+.|.
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred cCccCCCcceEeEecCCCCeECcCCc
Confidence 4667776543 2333455565553
No 257
>KOG0717|consensus
Probab=47.50 E-value=14 Score=24.22 Aligned_cols=21 Identities=29% Similarity=0.585 Sum_probs=17.6
Q ss_pred eecCcCcccccChHHHHHHHh
Q psy3500 75 YICQQCRDTFSSLYLFRNHLQ 95 (98)
Q Consensus 75 ~~C~~C~~~f~~~~~l~~H~~ 95 (98)
+-|..|.+.|....+|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 778999999998888888864
No 258
>PRK08197 threonine synthase; Validated
Probab=47.44 E-value=14 Score=23.46 Aligned_cols=24 Identities=17% Similarity=0.519 Sum_probs=17.4
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCc
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYH 27 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~ 27 (98)
++|..||+.+.... ..+.| .|+..
T Consensus 8 ~~C~~Cg~~~~~~~-~~~~C-~cg~~ 31 (394)
T PRK08197 8 LECSKCGETYDADQ-VHNLC-KCGKP 31 (394)
T ss_pred EEECCCCCCCCCCC-cceec-CCCCe
Confidence 57999999887533 36788 78644
No 259
>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=47.30 E-value=15 Score=15.45 Aligned_cols=12 Identities=33% Similarity=0.753 Sum_probs=6.7
Q ss_pred ecCcCcccccCh
Q psy3500 76 ICQQCRDTFSSL 87 (98)
Q Consensus 76 ~C~~C~~~f~~~ 87 (98)
.|+.|++.|...
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 455666655543
No 260
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=47.01 E-value=16 Score=24.42 Aligned_cols=7 Identities=43% Similarity=1.388 Sum_probs=3.3
Q ss_pred eecCCCc
Q psy3500 47 YKCEYCA 53 (98)
Q Consensus 47 ~~c~~c~ 53 (98)
+.|+.||
T Consensus 533 ~~CP~CG 539 (555)
T cd01675 533 FKCPKCG 539 (555)
T ss_pred CCCcCCC
Confidence 3444444
No 261
>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=46.73 E-value=20 Score=23.57 Aligned_cols=21 Identities=29% Similarity=0.713 Sum_probs=17.8
Q ss_pred eecCcCcccccChHHHHHHHh
Q psy3500 75 YICQQCRDTFSSLYLFRNHLQ 95 (98)
Q Consensus 75 ~~C~~C~~~f~~~~~l~~H~~ 95 (98)
|.|+.|.+.|.....+..|+.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~ 78 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHME 78 (466)
T ss_pred eeCCcccceeCCHHHHHHHHH
Confidence 678899999999988888874
No 262
>PRK12495 hypothetical protein; Provisional
Probab=46.66 E-value=18 Score=21.24 Aligned_cols=25 Identities=24% Similarity=0.571 Sum_probs=11.4
Q ss_pred CCCCCCCC-ccCCCCCCceecCCCCCcC
Q psy3500 2 YHCKTCST-LSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 2 ~~c~~c~~-~~~~~~~~~~~c~~C~~~~ 28 (98)
+.|..||. .|.-.|.. .|..|...+
T Consensus 43 ~hC~~CG~PIpa~pG~~--~Cp~CQ~~~ 68 (226)
T PRK12495 43 AHCDECGDPIFRHDGQE--FCPTCQQPV 68 (226)
T ss_pred hhcccccCcccCCCCee--ECCCCCCcc
Confidence 45666665 23222221 356665443
No 263
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=46.64 E-value=22 Score=18.02 Aligned_cols=34 Identities=18% Similarity=0.349 Sum_probs=18.3
Q ss_pred ceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCcccccc
Q psy3500 18 KYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQ 58 (98)
Q Consensus 18 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~ 58 (98)
-+.|+.|+.. .....+. .+.....|+.|+..+..
T Consensus 21 ~f~CP~Cge~-~v~v~~~------k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 21 IFECPRCGKV-SISVKIK------KNIAIITCGNCGLYTEF 54 (99)
T ss_pred EeECCCCCCe-EeeeecC------CCcceEECCCCCCccCE
Confidence 4788888832 1111111 13345678888865544
No 264
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=46.46 E-value=11 Score=24.58 Aligned_cols=16 Identities=13% Similarity=0.382 Sum_probs=11.3
Q ss_pred CCCceecCCCCCcCCC
Q psy3500 15 ISYKYTCYACDYHTLM 30 (98)
Q Consensus 15 ~~~~~~c~~C~~~~~~ 30 (98)
....|+|..|+..+..
T Consensus 422 ~~~~~~c~~c~~~yd~ 437 (479)
T PRK05452 422 LGPRMQCSVCQWIYDP 437 (479)
T ss_pred CCCeEEECCCCeEECC
Confidence 3456888888876654
No 265
>KOG2071|consensus
Probab=46.43 E-value=15 Score=24.71 Aligned_cols=26 Identities=27% Similarity=0.517 Sum_probs=21.2
Q ss_pred CCCeecCcCcccccChHHHHHHHhhh
Q psy3500 72 DKPYICQQCRDTFSSLYLFRNHLQSH 97 (98)
Q Consensus 72 ~~~~~C~~C~~~f~~~~~l~~H~~~h 97 (98)
..|-.|..||..|........|+..|
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhh
Confidence 45688999999999888887777665
No 266
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=46.11 E-value=26 Score=14.84 Aligned_cols=20 Identities=30% Similarity=0.843 Sum_probs=12.3
Q ss_pred CCCCCCccCCCCCCceecCCCC
Q psy3500 4 CKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
|+.|++. +.....|+|..|.
T Consensus 3 Cd~C~~~--~i~G~RykC~~C~ 22 (45)
T cd02339 3 CDTCRKQ--GIIGIRWKCAECP 22 (45)
T ss_pred CCCCCCC--CcccCeEECCCCC
Confidence 5556643 3345678888875
No 267
>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=45.95 E-value=0.34 Score=32.78 Aligned_cols=59 Identities=20% Similarity=0.421 Sum_probs=33.1
Q ss_pred cee-cCCCCCcCCCHHHHHHHHHHhcC-CCceecCCCccccccchhHHHHHHhhCCCCCeecCcCccc
Q psy3500 18 KYT-CYACDYHTLMSEDMKKHMRKHTG-EKPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDT 83 (98)
Q Consensus 18 ~~~-c~~C~~~~~~~~~l~~h~~~h~~-~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 83 (98)
||. |+.||..|.....|.-.. .++. ...-.|+.|.+.|....+ ++.| -.+..|+.||-.
T Consensus 89 pF~nCt~CGPr~~i~~~lpydr-~~t~m~~f~~C~~C~~ey~~p~~----rr~h--~~~~~C~~Cgp~ 149 (711)
T TIGR00143 89 PFISCTHCGPRFTIIEALPYDR-ENTSMADFPLCPDCAKEYKDPLD----RRFH--AQPIACPRCGPQ 149 (711)
T ss_pred CcccccCCCCCeEEeecCCCCC-CCcCCCCCcCCHHHHHHhcCCcc----ccCC--CCCccCCCCCcE
Confidence 444 889998886654433111 1111 122358888877766543 2223 336788888854
No 268
>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=45.74 E-value=15 Score=19.78 Aligned_cols=32 Identities=25% Similarity=0.664 Sum_probs=18.2
Q ss_pred ceecCCCccccccchhHHHHHHhhCCCCCeecCcCccccc
Q psy3500 46 PYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFS 85 (98)
Q Consensus 46 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 85 (98)
.+.|..|+..+.... +. ....|.|..|+..+.
T Consensus 123 ~~~C~~C~~~~~r~~------~~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKRHR------RS--KRKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeeeec------cc--chhhEECCCCCCEEE
Confidence 467777876653322 22 122378888876554
No 269
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=45.70 E-value=7.7 Score=17.49 Aligned_cols=8 Identities=25% Similarity=0.795 Sum_probs=3.7
Q ss_pred cCCCCCcC
Q psy3500 21 CYACDYHT 28 (98)
Q Consensus 21 c~~C~~~~ 28 (98)
|..||+..
T Consensus 7 CsTCGrDl 14 (63)
T PHA03082 7 CSTCGRDL 14 (63)
T ss_pred ecccCcch
Confidence 44454444
No 270
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=45.53 E-value=16 Score=24.77 Aligned_cols=7 Identities=29% Similarity=0.842 Sum_probs=3.7
Q ss_pred eecCCCC
Q psy3500 19 YTCYACD 25 (98)
Q Consensus 19 ~~c~~C~ 25 (98)
+.|+.||
T Consensus 547 ~~CP~CG 553 (586)
T TIGR02827 547 HRCPVCG 553 (586)
T ss_pred CcCcCCC
Confidence 4555554
No 271
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=45.05 E-value=7.1 Score=22.37 Aligned_cols=7 Identities=43% Similarity=1.540 Sum_probs=0.0
Q ss_pred CCCCCCC
Q psy3500 2 YHCKTCS 8 (98)
Q Consensus 2 ~~c~~c~ 8 (98)
|.|++||
T Consensus 102 y~CEICG 108 (196)
T PF11931_consen 102 YKCEICG 108 (196)
T ss_dssp -------
T ss_pred eeeEeCC
Confidence 7788888
No 272
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=44.77 E-value=29 Score=19.91 Aligned_cols=27 Identities=19% Similarity=0.497 Sum_probs=11.6
Q ss_pred CCCCCCCC---ccCCCCCCceecCCCCCcC
Q psy3500 2 YHCKTCST---LSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 2 ~~c~~c~~---~~~~~~~~~~~c~~C~~~~ 28 (98)
|.|+.|.. .|....+....|..|+..|
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~~C~~v~ 182 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCPKCKSVF 182 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCCcCcccc
Confidence 44555543 2233333344555554433
No 273
>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=44.60 E-value=10 Score=15.77 Aligned_cols=11 Identities=27% Similarity=1.047 Sum_probs=7.3
Q ss_pred CeecCcCcccc
Q psy3500 74 PYICQQCRDTF 84 (98)
Q Consensus 74 ~~~C~~C~~~f 84 (98)
+..|+.|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 46777777665
No 274
>KOG3002|consensus
Probab=44.32 E-value=47 Score=20.57 Aligned_cols=76 Identities=16% Similarity=0.158 Sum_probs=42.9
Q ss_pred CCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCC----CccccccchhHHHHHHhhCCCCCeecCcCcccc---cChH
Q psy3500 16 SYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEY----CAYSCTQSSALKIHERKHTGDKPYICQQCRDTF---SSLY 88 (98)
Q Consensus 16 ~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~----c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f---~~~~ 88 (98)
+++..|+.|.-.+.....+..-.. .......|+. |.+.|..... ..|.+.... +|+.|+.-+..- ....
T Consensus 78 ~~~~~CP~Cr~~~g~~R~~amEkV--~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~f-~~~~CP~p~~~C~~~G~~~ 153 (299)
T KOG3002|consen 78 KVSNKCPTCRLPIGNIRCRAMEKV--AEAVLVPCKNAKLGCTKSFPYGEK-SKHEKVCEF-RPCSCPVPGAECKYTGSYK 153 (299)
T ss_pred hhcccCCccccccccHHHHHHHHH--HHhceecccccccCCceeeccccc-ccccccccc-CCcCCCCCcccCCccCcHH
Confidence 456789999888877666554433 2333445543 6666666655 445555444 578887543211 2334
Q ss_pred HHHHHHh
Q psy3500 89 LFRNHLQ 95 (98)
Q Consensus 89 ~l~~H~~ 95 (98)
.+..|.+
T Consensus 154 ~l~~H~~ 160 (299)
T KOG3002|consen 154 DLYAHLN 160 (299)
T ss_pred HHHHHHH
Confidence 4555543
No 275
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=43.93 E-value=8.3 Score=17.39 Aligned_cols=8 Identities=25% Similarity=0.795 Sum_probs=3.7
Q ss_pred cCCCCCcC
Q psy3500 21 CYACDYHT 28 (98)
Q Consensus 21 c~~C~~~~ 28 (98)
|..||+..
T Consensus 7 CSTCGrDl 14 (63)
T PF05864_consen 7 CSTCGRDL 14 (63)
T ss_pred ecccCCcc
Confidence 44444444
No 276
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=43.75 E-value=19 Score=17.02 Aligned_cols=28 Identities=25% Similarity=0.518 Sum_probs=15.4
Q ss_pred CCCCCCC-----ccCCCCCCceecCCCCCcCCC
Q psy3500 3 HCKTCST-----LSRPNISYKYTCYACDYHTLM 30 (98)
Q Consensus 3 ~c~~c~~-----~~~~~~~~~~~c~~C~~~~~~ 30 (98)
.|+.|+. ++..++...-+|-.||.....
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~ 42 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYTERQ 42 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCeecc
Confidence 3666664 244444445567777755433
No 277
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=43.54 E-value=18 Score=25.18 Aligned_cols=8 Identities=25% Similarity=0.625 Sum_probs=4.1
Q ss_pred eecCCCCC
Q psy3500 19 YTCYACDY 26 (98)
Q Consensus 19 ~~c~~C~~ 26 (98)
+.|+.||.
T Consensus 694 ~~CP~CG~ 701 (735)
T PRK07111 694 DKCPKCGS 701 (735)
T ss_pred ccCcCCCC
Confidence 45555553
No 278
>PRK05638 threonine synthase; Validated
Probab=43.42 E-value=20 Score=23.21 Aligned_cols=24 Identities=17% Similarity=0.376 Sum_probs=17.3
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
++|..||+.+.. +..+.| .|+..+
T Consensus 2 l~C~~Cg~~~~~--~~~~~C-~c~~~l 25 (442)
T PRK05638 2 MKCPKCGREYNS--YIPPFC-ICGELL 25 (442)
T ss_pred eEeCCCCCCCCC--CCceec-CCCCcE
Confidence 579999999863 334889 797443
No 279
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=42.25 E-value=19 Score=19.41 Aligned_cols=10 Identities=40% Similarity=1.026 Sum_probs=5.2
Q ss_pred CCCCCCccCC
Q psy3500 4 CKTCSTLSRP 13 (98)
Q Consensus 4 c~~c~~~~~~ 13 (98)
|+-||..|-+
T Consensus 32 C~~CG~v~~P 41 (140)
T COG1545 32 CKKCGRVYFP 41 (140)
T ss_pred cCCCCeEEcC
Confidence 5555555444
No 280
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.22 E-value=28 Score=18.54 Aligned_cols=12 Identities=17% Similarity=0.282 Sum_probs=5.6
Q ss_pred ceecCCCCCcCC
Q psy3500 18 KYTCYACDYHTL 29 (98)
Q Consensus 18 ~~~c~~C~~~~~ 29 (98)
|--|..||..|+
T Consensus 68 psfchncgs~fp 79 (160)
T COG4306 68 PSFCHNCGSRFP 79 (160)
T ss_pred cchhhcCCCCCC
Confidence 333555555553
No 281
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=41.95 E-value=47 Score=19.22 Aligned_cols=11 Identities=27% Similarity=0.591 Sum_probs=6.6
Q ss_pred ceecCCCcccc
Q psy3500 46 PYKCEYCAYSC 56 (98)
Q Consensus 46 ~~~c~~c~~~~ 56 (98)
...|..||..+
T Consensus 30 lvrC~eCG~V~ 40 (201)
T COG1326 30 LVRCEECGTVH 40 (201)
T ss_pred EEEccCCCcEe
Confidence 35666666554
No 282
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=41.87 E-value=22 Score=23.98 Aligned_cols=8 Identities=25% Similarity=0.625 Sum_probs=4.5
Q ss_pred eecCCCCC
Q psy3500 19 YTCYACDY 26 (98)
Q Consensus 19 ~~c~~C~~ 26 (98)
+.|+.||.
T Consensus 539 ~~CP~Cgs 546 (579)
T TIGR02487 539 DKCPKCGS 546 (579)
T ss_pred CcCcCCCC
Confidence 45666653
No 283
>PF11228 DUF3027: Protein of unknown function (DUF3027); InterPro: IPR021391 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=41.82 E-value=20 Score=20.53 Aligned_cols=27 Identities=19% Similarity=0.182 Sum_probs=13.6
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
..|.+||....-.+.+.....+|.+.+
T Consensus 146 ~~C~tCgF~~plaG~L~~~FGVCaNe~ 172 (193)
T PF11228_consen 146 AQCSTCGFYVPLAGSLGQMFGVCANEW 172 (193)
T ss_pred cCCCcCccceEcCCchhcceeeecCCC
Confidence 455666655444444444445554444
No 284
>PRK05580 primosome assembly protein PriA; Validated
Probab=41.49 E-value=34 Score=23.61 Aligned_cols=6 Identities=33% Similarity=1.104 Sum_probs=2.6
Q ss_pred ecCCCc
Q psy3500 48 KCEYCA 53 (98)
Q Consensus 48 ~c~~c~ 53 (98)
.|+.|+
T Consensus 423 ~Cp~Cg 428 (679)
T PRK05580 423 ACPECG 428 (679)
T ss_pred CCCCCc
Confidence 344443
No 285
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=41.25 E-value=19 Score=18.38 Aligned_cols=40 Identities=23% Similarity=0.391 Sum_probs=21.5
Q ss_pred CCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCcccccc
Q psy3500 15 ISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQ 58 (98)
Q Consensus 15 ~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~ 58 (98)
.++.|.|+.|+..-.....++. ........|..||..|.-
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk----~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKK----TVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred CCceEecCccCCeeeeEEEEEe----cCceeEEEcccCcceEEE
Confidence 4566888888754433222221 112234678888876643
No 286
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=40.80 E-value=22 Score=24.30 Aligned_cols=8 Identities=25% Similarity=0.642 Sum_probs=4.3
Q ss_pred eecCCCCC
Q psy3500 19 YTCYACDY 26 (98)
Q Consensus 19 ~~c~~C~~ 26 (98)
+.|+.|+.
T Consensus 583 ~~CP~CGs 590 (625)
T PRK08579 583 TRCPRCGS 590 (625)
T ss_pred CcCcCCCC
Confidence 45555554
No 287
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=40.16 E-value=27 Score=16.92 Aligned_cols=50 Identities=18% Similarity=0.321 Sum_probs=16.1
Q ss_pred CCCCCCCc--cCCCCCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccc
Q psy3500 3 HCKTCSTL--SRPNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCT 57 (98)
Q Consensus 3 ~c~~c~~~--~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~ 57 (98)
.|++||.. ...+|+.--.|.+|+...- ..-...-+ . +....|+.|...|.
T Consensus 11 iCqiCGD~VGl~~~Ge~FVAC~eC~fPvC--r~CyEYEr-k--eg~q~CpqCkt~yk 62 (80)
T PF14569_consen 11 ICQICGDDVGLTENGEVFVACHECAFPVC--RPCYEYER-K--EGNQVCPQCKTRYK 62 (80)
T ss_dssp B-SSS--B--B-SSSSB--S-SSS-------HHHHHHHH-H--TS-SB-TTT--B--
T ss_pred ccccccCccccCCCCCEEEEEcccCCccc--hhHHHHHh-h--cCcccccccCCCcc
Confidence 57888853 4566776556777753322 22111111 1 22346777775444
No 288
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=39.95 E-value=5.6 Score=20.21 Aligned_cols=20 Identities=20% Similarity=0.584 Sum_probs=12.1
Q ss_pred CCCCCCCCc--------cCCCCCCceec
Q psy3500 2 YHCKTCSTL--------SRPNISYKYTC 21 (98)
Q Consensus 2 ~~c~~c~~~--------~~~~~~~~~~c 21 (98)
|+|-.||.- |...|-..|.|
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C 30 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYEC 30 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHH
Confidence 678888852 33445555655
No 289
>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=39.81 E-value=13 Score=20.20 Aligned_cols=11 Identities=27% Similarity=0.851 Sum_probs=5.4
Q ss_pred eecCCCccccc
Q psy3500 47 YKCEYCAYSCT 57 (98)
Q Consensus 47 ~~c~~c~~~~~ 57 (98)
|.|..|...|.
T Consensus 131 ~~c~~c~epf~ 141 (146)
T TIGR02159 131 YRCRACKEPFE 141 (146)
T ss_pred hhhhhhCCcHh
Confidence 44555554443
No 290
>PTZ00448 hypothetical protein; Provisional
Probab=39.42 E-value=27 Score=22.23 Aligned_cols=23 Identities=22% Similarity=0.574 Sum_probs=19.0
Q ss_pred CeecCcCcccccChHHHHHHHhh
Q psy3500 74 PYICQQCRDTFSSLYLFRNHLQS 96 (98)
Q Consensus 74 ~~~C~~C~~~f~~~~~l~~H~~~ 96 (98)
.|.|..|+-.|......+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999888888888764
No 291
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=39.38 E-value=6.8 Score=15.61 Aligned_cols=24 Identities=29% Similarity=0.829 Sum_probs=10.2
Q ss_pred CCCCCCccCCCCC--CceecCCCCCc
Q psy3500 4 CKTCSTLSRPNIS--YKYTCYACDYH 27 (98)
Q Consensus 4 c~~c~~~~~~~~~--~~~~c~~C~~~ 27 (98)
|+.||-+-.+..+ ....|..|+..
T Consensus 4 Cp~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 4 CPECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp ETTTTSBEEEEEETTTTEEESSSS-E
T ss_pred CCCCCccceEcCCCccCcCCCCCCCc
Confidence 5566654432221 11156666543
No 292
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=39.06 E-value=24 Score=18.20 Aligned_cols=27 Identities=15% Similarity=0.267 Sum_probs=17.0
Q ss_pred CCCCCCCccCCCCCCceecCCCCCcCC
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACDYHTL 29 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~~~~~ 29 (98)
.|+.|+.-+.-.....+.|++|..-+.
T Consensus 5 ~cp~c~sEytYed~~~~~cpec~~ew~ 31 (112)
T COG2824 5 PCPKCNSEYTYEDGGQLICPECAHEWN 31 (112)
T ss_pred CCCccCCceEEecCceEeCchhccccc
Confidence 466666655533334778888876665
No 293
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=38.94 E-value=16 Score=19.13 Aligned_cols=11 Identities=18% Similarity=0.567 Sum_probs=6.2
Q ss_pred ceecCCCCCcC
Q psy3500 18 KYTCYACDYHT 28 (98)
Q Consensus 18 ~~~c~~C~~~~ 28 (98)
..+|..|+..+
T Consensus 70 ~~~C~~C~~~~ 80 (115)
T COG0375 70 ECWCLDCGQEV 80 (115)
T ss_pred EEEeccCCCee
Confidence 35677775443
No 294
>KOG3362|consensus
Probab=38.46 E-value=12 Score=20.33 Aligned_cols=20 Identities=30% Similarity=0.639 Sum_probs=12.1
Q ss_pred eecCCCccccccchhHHHHH
Q psy3500 47 YKCEYCAYSCTQSSALKIHE 66 (98)
Q Consensus 47 ~~c~~c~~~~~~~~~l~~h~ 66 (98)
|.|..||..+-+..-+..|.
T Consensus 130 ysC~~CG~kyCsv~C~~~Hn 149 (156)
T KOG3362|consen 130 YSCVNCGTKYCSVRCLKTHN 149 (156)
T ss_pred hHHHhcCCceeechhhhhcc
Confidence 55666776666665555543
No 295
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=38.46 E-value=11 Score=14.16 Aligned_cols=7 Identities=29% Similarity=1.132 Sum_probs=3.3
Q ss_pred CCCCCCC
Q psy3500 3 HCKTCST 9 (98)
Q Consensus 3 ~c~~c~~ 9 (98)
.|..|..
T Consensus 6 ~C~~C~~ 12 (30)
T PF00641_consen 6 KCPSCTF 12 (30)
T ss_dssp EETTTTE
T ss_pred cCCCCcC
Confidence 4555543
No 296
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=38.40 E-value=14 Score=16.59 Aligned_cols=9 Identities=33% Similarity=1.010 Sum_probs=2.0
Q ss_pred CCCCCCCCc
Q psy3500 2 YHCKTCSTL 10 (98)
Q Consensus 2 ~~c~~c~~~ 10 (98)
|+|++||..
T Consensus 34 y~Cp~CgAt 42 (55)
T PF05741_consen 34 YVCPICGAT 42 (55)
T ss_dssp ---TTT---
T ss_pred CcCCCCcCc
Confidence 566666653
No 297
>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=37.95 E-value=30 Score=19.16 Aligned_cols=15 Identities=20% Similarity=0.499 Sum_probs=7.3
Q ss_pred CceecCCCccccccc
Q psy3500 45 KPYKCEYCAYSCTQS 59 (98)
Q Consensus 45 ~~~~c~~c~~~~~~~ 59 (98)
.|.-|..||+.|.+.
T Consensus 67 ~PsYC~~CGkpyPWt 81 (158)
T PF10083_consen 67 APSYCHNCGKPYPWT 81 (158)
T ss_pred CChhHHhCCCCCchH
Confidence 344455555555443
No 298
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=37.90 E-value=43 Score=15.11 Aligned_cols=22 Identities=23% Similarity=0.706 Sum_probs=12.7
Q ss_pred CCCCCCccCCCCCC----ceecCCCC
Q psy3500 4 CKTCSTLSRPNISY----KYTCYACD 25 (98)
Q Consensus 4 c~~c~~~~~~~~~~----~~~c~~C~ 25 (98)
|+.|++...+.... .|+|+.|.
T Consensus 8 CE~C~~dLp~~s~~A~ICSfECTFC~ 33 (57)
T PF06906_consen 8 CECCDKDLPPDSPEAYICSFECTFCA 33 (57)
T ss_pred ccccCCCCCCCCCcceEEeEeCcccH
Confidence 67777766654421 46666553
No 299
>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=37.88 E-value=16 Score=19.68 Aligned_cols=18 Identities=39% Similarity=0.864 Sum_probs=13.5
Q ss_pred hhCCCCCeecCcCcccccC
Q psy3500 68 KHTGDKPYICQQCRDTFSS 86 (98)
Q Consensus 68 ~~~~~~~~~C~~C~~~f~~ 86 (98)
.+.+ ++.+|+.||..|..
T Consensus 107 l~~g-~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 107 LHKG-KPQRCPECGQVFKL 124 (136)
T ss_dssp EETT-SEEEETTTEEEEEE
T ss_pred EeCC-CccCCCCCCeEEEE
Confidence 4455 48999999988764
No 300
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=37.84 E-value=14 Score=17.50 Aligned_cols=25 Identities=24% Similarity=0.444 Sum_probs=12.6
Q ss_pred CCCCCCCccCCCCCCceecCCCCCcC
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
.|+.|..-....+ -.|.|..|+..|
T Consensus 3 ~CP~C~~~L~~~~-~~~~C~~C~~~~ 27 (70)
T PF07191_consen 3 TCPKCQQELEWQG-GHYHCEACQKDY 27 (70)
T ss_dssp B-SSS-SBEEEET-TEEEETTT--EE
T ss_pred cCCCCCCccEEeC-CEEECccccccc
Confidence 4666766554444 467777777654
No 301
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=37.62 E-value=15 Score=15.03 Aligned_cols=11 Identities=27% Similarity=1.005 Sum_probs=6.3
Q ss_pred eecCcCccccc
Q psy3500 75 YICQQCRDTFS 85 (98)
Q Consensus 75 ~~C~~C~~~f~ 85 (98)
+.|+.||..+.
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 55666665543
No 302
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=37.43 E-value=23 Score=18.21 Aligned_cols=22 Identities=18% Similarity=0.366 Sum_probs=14.4
Q ss_pred CeecCcCcccccChHHHHHHHh
Q psy3500 74 PYICQQCRDTFSSLYLFRNHLQ 95 (98)
Q Consensus 74 ~~~C~~C~~~f~~~~~l~~H~~ 95 (98)
.+-|-+|.+-|.....|..|.+
T Consensus 55 qhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhc
Confidence 3566667777777766666654
No 303
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=37.05 E-value=26 Score=18.95 Aligned_cols=23 Identities=26% Similarity=0.184 Sum_probs=13.7
Q ss_pred eecCCCccccccchhHHHHHHhhCCC
Q psy3500 47 YKCEYCAYSCTQSSALKIHERKHTGD 72 (98)
Q Consensus 47 ~~c~~c~~~~~~~~~l~~h~~~~~~~ 72 (98)
..|-.+|+.|.+ |.+|+..|.+-
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gm 99 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGL 99 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCC
Confidence 446666666655 56666665553
No 304
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=37.01 E-value=40 Score=20.10 Aligned_cols=25 Identities=16% Similarity=0.400 Sum_probs=16.2
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
|.|++|+.-... .+..+.|.. +..|
T Consensus 3 ~~CP~C~~~l~~-~~~~~~C~~-~h~f 27 (272)
T PRK11088 3 YQCPLCHQPLTL-EENSWICPQ-NHQF 27 (272)
T ss_pred ccCCCCCcchhc-CCCEEEcCC-CCCC
Confidence 889999987643 334566654 4445
No 305
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=36.88 E-value=33 Score=13.30 Aligned_cols=22 Identities=32% Similarity=0.694 Sum_probs=13.1
Q ss_pred CCCCCCc-cCCCCCCceecCCCC
Q psy3500 4 CKTCSTL-SRPNISYKYTCYACD 25 (98)
Q Consensus 4 c~~c~~~-~~~~~~~~~~c~~C~ 25 (98)
|.-|+.. .-+.+...++|..|.
T Consensus 4 C~~C~t~L~yP~gA~~vrCs~C~ 26 (31)
T TIGR01053 4 CGGCRTLLMYPRGASSVRCALCQ 26 (31)
T ss_pred cCCCCcEeecCCCCCeEECCCCC
Confidence 5556653 335566677777775
No 306
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=36.87 E-value=9.6 Score=15.45 Aligned_cols=13 Identities=23% Similarity=0.664 Sum_probs=6.1
Q ss_pred ecCcCcccccChH
Q psy3500 76 ICQQCRDTFSSLY 88 (98)
Q Consensus 76 ~C~~C~~~f~~~~ 88 (98)
.|+.|++.|-+.+
T Consensus 4 ~CprC~kg~Hwa~ 16 (36)
T PF14787_consen 4 LCPRCGKGFHWAS 16 (36)
T ss_dssp C-TTTSSSCS-TT
T ss_pred cCcccCCCcchhh
Confidence 4566666655443
No 307
>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=36.69 E-value=37 Score=18.34 Aligned_cols=46 Identities=15% Similarity=0.193 Sum_probs=25.7
Q ss_pred eecCCCCCcCCCHHHHHHHHHH-----hcCCCceecCCCccccccchhHHH
Q psy3500 19 YTCYACDYHTLMSEDMKKHMRK-----HTGEKPYKCEYCAYSCTQSSALKI 64 (98)
Q Consensus 19 ~~c~~C~~~~~~~~~l~~h~~~-----h~~~~~~~c~~c~~~~~~~~~l~~ 64 (98)
-.|..|+......+.-..--.+ .....-+.|+.|++.|...+...+
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHH
Confidence 4688887655332221110001 112335889999999988776544
No 308
>PF14369 zf-RING_3: zinc-finger
Probab=36.40 E-value=18 Score=14.44 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=5.8
Q ss_pred ecCcCccccc
Q psy3500 76 ICQQCRDTFS 85 (98)
Q Consensus 76 ~C~~C~~~f~ 85 (98)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4666665553
No 309
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=36.19 E-value=21 Score=18.20 Aligned_cols=25 Identities=16% Similarity=0.390 Sum_probs=11.8
Q ss_pred CCCCCC-ccCCCCCCceecCCCCCcCC
Q psy3500 4 CKTCST-LSRPNISYKYTCYACDYHTL 29 (98)
Q Consensus 4 c~~c~~-~~~~~~~~~~~c~~C~~~~~ 29 (98)
|+.|+. .|...++ .-.|..|+..|.
T Consensus 38 CeiC~~~GY~q~g~-~lvC~~C~~~~~ 63 (102)
T PF10080_consen 38 CEICGPKGYYQEGD-QLVCKNCGVRFN 63 (102)
T ss_pred ccccCCCceEEECC-EEEEecCCCEEe
Confidence 555542 2332222 345666666553
No 310
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=36.08 E-value=33 Score=14.75 Aligned_cols=21 Identities=19% Similarity=0.717 Sum_probs=12.8
Q ss_pred CCCCCCCccCCCCCCceecCCCC
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
.|+.|++. +-.+..|+|..|.
T Consensus 2 ~C~~C~~~--~i~g~R~~C~~C~ 22 (49)
T cd02345 2 SCSACRKQ--DISGIRFPCQVCR 22 (49)
T ss_pred cCCCCCCC--CceEeeEECCCCC
Confidence 36666663 2224778888885
No 311
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=35.98 E-value=36 Score=17.64 Aligned_cols=10 Identities=20% Similarity=1.029 Sum_probs=5.0
Q ss_pred CCCeecCcCc
Q psy3500 72 DKPYICQQCR 81 (98)
Q Consensus 72 ~~~~~C~~C~ 81 (98)
+..|.|..|-
T Consensus 92 ~~~WlC~vC~ 101 (118)
T PF02318_consen 92 EPIWLCKVCQ 101 (118)
T ss_dssp SCCEEEHHHH
T ss_pred CCCEEChhhH
Confidence 3345555553
No 312
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=35.96 E-value=23 Score=21.79 Aligned_cols=11 Identities=36% Similarity=0.851 Sum_probs=5.1
Q ss_pred eecCCCccccc
Q psy3500 47 YKCEYCAYSCT 57 (98)
Q Consensus 47 ~~c~~c~~~~~ 57 (98)
+.|+.|+..|.
T Consensus 58 ~vcp~c~~h~r 68 (296)
T CHL00174 58 NICEQCGYHLK 68 (296)
T ss_pred CCCCCCCCCcC
Confidence 34555554443
No 313
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=35.96 E-value=18 Score=18.04 Aligned_cols=31 Identities=26% Similarity=0.811 Sum_probs=20.8
Q ss_pred CceecCCCccccccchhHHHHHHhhCCCCCeecCcCccccc
Q psy3500 45 KPYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTFS 85 (98)
Q Consensus 45 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 85 (98)
..|.|+.|++.-... ...| -|.|..|++.|.
T Consensus 34 ~ky~Cp~Cgk~~vkR--------~a~G--IW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKR--------VATG--IWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEEEE--------EETT--EEEETTTTEEEE
T ss_pred CCCcCCCCCCceeEE--------eeeE--EeecCCCCCEEe
Confidence 468999999753221 2233 599999998875
No 314
>KOG2923|consensus
Probab=35.89 E-value=29 Score=16.11 Aligned_cols=33 Identities=21% Similarity=0.483 Sum_probs=19.0
Q ss_pred ceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCcccc
Q psy3500 18 KYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSC 56 (98)
Q Consensus 18 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~ 56 (98)
-|.|+ ||-.|.....- .-.++.-..|+-|+...
T Consensus 22 ~yPCp-CGDrf~It~ed-----L~~ge~Va~CpsCSL~I 54 (67)
T KOG2923|consen 22 YYPCP-CGDRFQITLED-----LENGEDVARCPSCSLII 54 (67)
T ss_pred EcCCC-CCCeeeecHHH-----HhCCCeeecCCCceEEE
Confidence 46664 77676543221 23466667888887543
No 315
>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=35.86 E-value=9.7 Score=15.32 Aligned_cols=9 Identities=22% Similarity=0.792 Sum_probs=4.8
Q ss_pred CCCCCCCcc
Q psy3500 3 HCKTCSTLS 11 (98)
Q Consensus 3 ~c~~c~~~~ 11 (98)
.|+.||+.+
T Consensus 3 ~C~~Cg~~Y 11 (36)
T PF05191_consen 3 ICPKCGRIY 11 (36)
T ss_dssp EETTTTEEE
T ss_pred CcCCCCCcc
Confidence 455566544
No 316
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=35.60 E-value=39 Score=13.73 Aligned_cols=25 Identities=12% Similarity=0.024 Sum_probs=11.0
Q ss_pred CCCCCCccCCCCCCceecCCCCCcCCC
Q psy3500 4 CKTCSTLSRPNISYKYTCYACDYHTLM 30 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~~~~~~ 30 (98)
|.+|-..+.. ++.....+ |+..|-.
T Consensus 3 C~IC~~~~~~-~~~~~~l~-C~H~fh~ 27 (44)
T PF13639_consen 3 CPICLEEFED-GEKVVKLP-CGHVFHR 27 (44)
T ss_dssp ETTTTCBHHT-TSCEEEET-TSEEEEH
T ss_pred CcCCChhhcC-CCeEEEcc-CCCeeCH
Confidence 4555555543 22233333 5555533
No 317
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=35.47 E-value=18 Score=20.42 Aligned_cols=8 Identities=25% Similarity=0.837 Sum_probs=2.1
Q ss_pred CCCCCCcc
Q psy3500 4 CKTCSTLS 11 (98)
Q Consensus 4 c~~c~~~~ 11 (98)
|..||..|
T Consensus 137 C~~C~~~f 144 (175)
T PF05280_consen 137 CRRCGGHF 144 (175)
T ss_dssp -TTT--EE
T ss_pred CCCCCCCe
Confidence 44444433
No 318
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=34.85 E-value=23 Score=20.94 Aligned_cols=15 Identities=27% Similarity=0.603 Sum_probs=11.7
Q ss_pred CCCeecCcCcccccC
Q psy3500 72 DKPYICQQCRDTFSS 86 (98)
Q Consensus 72 ~~~~~C~~C~~~f~~ 86 (98)
.++.+|++||..|..
T Consensus 179 GkpqRCpECGqVFKL 193 (268)
T PTZ00043 179 GFLYRCGECDQIFML 193 (268)
T ss_pred CCCccCCCCCcEEEE
Confidence 347999999987753
No 319
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=34.55 E-value=48 Score=14.51 Aligned_cols=13 Identities=31% Similarity=0.823 Sum_probs=8.3
Q ss_pred CCCCCeecCcCcc
Q psy3500 70 TGDKPYICQQCRD 82 (98)
Q Consensus 70 ~~~~~~~C~~C~~ 82 (98)
.++....|+.||+
T Consensus 42 ~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 42 KGDEIVFCPNCGR 54 (56)
T ss_pred cCCCeEECcCCCc
Confidence 3345677777775
No 320
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=34.25 E-value=35 Score=14.62 Aligned_cols=21 Identities=24% Similarity=0.746 Sum_probs=12.2
Q ss_pred CCCCCCCccCCCCCCceecCCCC
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
.|+.|++.... ...|+|..|.
T Consensus 2 ~C~~C~~~~i~--g~R~~C~~C~ 22 (49)
T cd02338 2 SCDGCGKSNFT--GRRYKCLICY 22 (49)
T ss_pred CCCCCcCCCcE--EeeEEeCCCC
Confidence 36666643222 4677887774
No 321
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=34.14 E-value=25 Score=13.38 Aligned_cols=8 Identities=25% Similarity=1.223 Sum_probs=3.8
Q ss_pred CCCCCCCC
Q psy3500 2 YHCKTCST 9 (98)
Q Consensus 2 ~~c~~c~~ 9 (98)
|.|..|++
T Consensus 28 f~C~~C~~ 35 (39)
T smart00132 28 FKCSKCGK 35 (39)
T ss_pred CCCcccCC
Confidence 34555544
No 322
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=34.10 E-value=23 Score=20.48 Aligned_cols=11 Identities=27% Similarity=0.739 Sum_probs=6.5
Q ss_pred eecCCCCCcCC
Q psy3500 19 YTCYACDYHTL 29 (98)
Q Consensus 19 ~~c~~C~~~~~ 29 (98)
+.|..||.++.
T Consensus 44 ~~C~~CgYR~~ 54 (201)
T COG1779 44 GVCERCGYRST 54 (201)
T ss_pred EEccccCCccc
Confidence 55666665543
No 323
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=34.08 E-value=33 Score=14.73 Aligned_cols=12 Identities=17% Similarity=0.684 Sum_probs=7.4
Q ss_pred CCCCCCCCccCC
Q psy3500 2 YHCKTCSTLSRP 13 (98)
Q Consensus 2 ~~c~~c~~~~~~ 13 (98)
|.|..|++.+..
T Consensus 27 f~C~~C~~~l~~ 38 (58)
T PF00412_consen 27 FKCSKCGKPLND 38 (58)
T ss_dssp SBETTTTCBTTT
T ss_pred cccCCCCCccCC
Confidence 566777765544
No 324
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=33.97 E-value=17 Score=14.33 Aligned_cols=8 Identities=38% Similarity=1.232 Sum_probs=4.1
Q ss_pred CCCCCCCC
Q psy3500 2 YHCKTCST 9 (98)
Q Consensus 2 ~~c~~c~~ 9 (98)
|+|..|++
T Consensus 9 Y~C~~C~~ 16 (32)
T PF13696_consen 9 YVCHRCGQ 16 (32)
T ss_pred CEeecCCC
Confidence 45555554
No 325
>PLN02569 threonine synthase
Probab=33.84 E-value=33 Score=22.72 Aligned_cols=25 Identities=8% Similarity=-0.035 Sum_probs=17.4
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCcC
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYHT 28 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~~ 28 (98)
++|..||+.+.. .+..|.| .|+..+
T Consensus 50 l~C~~Cg~~y~~-~~~~~~C-~cgg~l 74 (484)
T PLN02569 50 LECPLTGEKYSL-DEVVYRS-KSGGLL 74 (484)
T ss_pred cEeCCCCCcCCC-ccccccC-CCCCeE
Confidence 578889988755 4456788 686544
No 326
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=33.61 E-value=26 Score=13.39 Aligned_cols=11 Identities=27% Similarity=0.990 Sum_probs=4.9
Q ss_pred CeecCcCcccc
Q psy3500 74 PYICQQCRDTF 84 (98)
Q Consensus 74 ~~~C~~C~~~f 84 (98)
.|.|+.|+..+
T Consensus 13 kY~Cp~C~~~~ 23 (30)
T PF04438_consen 13 KYRCPRCGARY 23 (30)
T ss_dssp SEE-TTT--EE
T ss_pred EEECCCcCCce
Confidence 47777776543
No 327
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=33.59 E-value=37 Score=18.59 Aligned_cols=10 Identities=30% Similarity=0.916 Sum_probs=5.0
Q ss_pred ceecCCCCCc
Q psy3500 18 KYTCYACDYH 27 (98)
Q Consensus 18 ~~~c~~C~~~ 27 (98)
.|.|..|+..
T Consensus 51 ~~~C~~C~~~ 60 (166)
T cd04476 51 TYRCEKCNKS 60 (166)
T ss_pred cEECCCCCCc
Confidence 4555555543
No 328
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.53 E-value=40 Score=20.60 Aligned_cols=8 Identities=25% Similarity=1.173 Sum_probs=3.9
Q ss_pred eecCcCcc
Q psy3500 75 YICQQCRD 82 (98)
Q Consensus 75 ~~C~~C~~ 82 (98)
|.|+.|..
T Consensus 256 yvCs~Cls 263 (279)
T TIGR00627 256 FVCSVCLS 263 (279)
T ss_pred EECCCccC
Confidence 55555443
No 329
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=33.42 E-value=49 Score=14.31 Aligned_cols=21 Identities=29% Similarity=1.013 Sum_probs=12.4
Q ss_pred CCCCCCCccCCCCCCceecCCCC
Q psy3500 3 HCKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
.|+.|++. +.....|+|..|.
T Consensus 2 ~Cd~C~~~--pi~g~RykC~~C~ 22 (49)
T cd02334 2 KCNICKEF--PITGFRYRCLKCF 22 (49)
T ss_pred CCCCCCCC--CceeeeEECCCCC
Confidence 36666653 2234678888775
No 330
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=33.04 E-value=27 Score=18.01 Aligned_cols=13 Identities=23% Similarity=0.490 Sum_probs=7.3
Q ss_pred CCCceecCCCCCc
Q psy3500 15 ISYKYTCYACDYH 27 (98)
Q Consensus 15 ~~~~~~c~~C~~~ 27 (98)
|...+.|..|+..
T Consensus 39 G~~~~~C~~Cg~~ 51 (111)
T PF14319_consen 39 GFHRYRCEDCGHE 51 (111)
T ss_pred CcceeecCCCCce
Confidence 4445666666643
No 331
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=33.03 E-value=29 Score=17.08 Aligned_cols=11 Identities=18% Similarity=0.443 Sum_probs=7.3
Q ss_pred CCCCCCCccCC
Q psy3500 3 HCKTCSTLSRP 13 (98)
Q Consensus 3 ~c~~c~~~~~~ 13 (98)
+|+.||..+.+
T Consensus 10 ~C~~CG~d~~~ 20 (86)
T PF06170_consen 10 RCPHCGLDYSH 20 (86)
T ss_pred cccccCCcccc
Confidence 57778776553
No 332
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=32.85 E-value=26 Score=21.50 Aligned_cols=12 Identities=17% Similarity=0.346 Sum_probs=6.6
Q ss_pred eecCCCcccccc
Q psy3500 47 YKCEYCAYSCTQ 58 (98)
Q Consensus 47 ~~c~~c~~~~~~ 58 (98)
+.|+.|+..|.-
T Consensus 47 ~vc~~c~~h~rl 58 (292)
T PRK05654 47 NVCPKCGHHMRI 58 (292)
T ss_pred CCCCCCCCCeeC
Confidence 456666655543
No 333
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=32.50 E-value=40 Score=14.77 Aligned_cols=15 Identities=20% Similarity=0.450 Sum_probs=8.8
Q ss_pred CCceecCCCcccccc
Q psy3500 44 EKPYKCEYCAYSCTQ 58 (98)
Q Consensus 44 ~~~~~c~~c~~~~~~ 58 (98)
.....|+.|+..|-.
T Consensus 38 ~~~v~C~~C~~~fC~ 52 (64)
T smart00647 38 CNRVTCPKCGFSFCF 52 (64)
T ss_pred CCeeECCCCCCeECC
Confidence 344667667666544
No 334
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=32.43 E-value=68 Score=19.84 Aligned_cols=23 Identities=35% Similarity=0.574 Sum_probs=16.8
Q ss_pred CceecCCCccccccchhHHHHHH
Q psy3500 45 KPYKCEYCAYSCTQSSALKIHER 67 (98)
Q Consensus 45 ~~~~c~~c~~~~~~~~~l~~h~~ 67 (98)
.-|.|..|-+.|.....+.+|+.
T Consensus 47 ~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 47 KLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred eEEEcCCCcchhCCHHHHHHHHH
Confidence 45777777777777777777765
No 335
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=31.78 E-value=72 Score=23.66 Aligned_cols=50 Identities=12% Similarity=0.263 Sum_probs=29.0
Q ss_pred CCCCCCCc--cCCCCCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccc
Q psy3500 3 HCKTCSTL--SRPNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCT 57 (98)
Q Consensus 3 ~c~~c~~~--~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~ 57 (98)
.|++||-. ...+|+.--.|.+|+...-...- .. -..+....|++|...|.
T Consensus 19 iCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY--EY---Er~eG~q~CPqCktrYk 70 (1079)
T PLN02638 19 VCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY--EY---ERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred eeeecccccCcCCCCCEEEEeccCCCccccchh--hh---hhhcCCccCCccCCchh
Confidence 69999963 45677765668888754433322 11 11223356888876665
No 336
>PF09965 DUF2199: Uncharacterized protein conserved in bacteria (DUF2199); InterPro: IPR018697 This domain has no known function.
Probab=31.72 E-value=26 Score=19.18 Aligned_cols=11 Identities=27% Similarity=0.842 Sum_probs=8.5
Q ss_pred CCCCCCCCccC
Q psy3500 2 YHCKTCSTLSR 12 (98)
Q Consensus 2 ~~c~~c~~~~~ 12 (98)
|.|.+||+...
T Consensus 1 y~C~~Cg~~h~ 11 (148)
T PF09965_consen 1 YTCSCCGEEHE 11 (148)
T ss_pred CCCCcCCccCC
Confidence 78999997653
No 337
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=31.60 E-value=31 Score=22.09 Aligned_cols=26 Identities=23% Similarity=0.584 Sum_probs=13.0
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCc
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYH 27 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~ 27 (98)
|.|+.||+...-..+..-+|+.||..
T Consensus 241 ~~c~~cg~~~~~~~~~~~~c~~Cg~~ 266 (380)
T COG1867 241 YHCSRCGEIVGSFREVDEKCPHCGGK 266 (380)
T ss_pred EEcccccceecccccccccCCccccc
Confidence 56777773322222333456666643
No 338
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=31.45 E-value=40 Score=14.72 Aligned_cols=11 Identities=18% Similarity=0.519 Sum_probs=5.7
Q ss_pred eecCCCccccc
Q psy3500 47 YKCEYCAYSCT 57 (98)
Q Consensus 47 ~~c~~c~~~~~ 57 (98)
..|+.|+..|-
T Consensus 41 ~~C~~C~~~fC 51 (64)
T PF01485_consen 41 VTCPSCGTEFC 51 (64)
T ss_dssp CCTTSCCSEEC
T ss_pred eECCCCCCcCc
Confidence 45555555443
No 339
>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=31.30 E-value=14 Score=22.54 Aligned_cols=11 Identities=18% Similarity=0.371 Sum_probs=5.2
Q ss_pred eecCCCccccc
Q psy3500 47 YKCEYCAYSCT 57 (98)
Q Consensus 47 ~~c~~c~~~~~ 57 (98)
+.|+.|+..|.
T Consensus 46 ~vc~~c~~h~r 56 (285)
T TIGR00515 46 EVCPKCDHHMR 56 (285)
T ss_pred CCCCCCCCcCc
Confidence 34555554443
No 340
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=31.18 E-value=18 Score=22.80 Aligned_cols=12 Identities=25% Similarity=0.753 Sum_probs=6.3
Q ss_pred ceecCCCCCcCC
Q psy3500 18 KYTCYACDYHTL 29 (98)
Q Consensus 18 ~~~c~~C~~~~~ 29 (98)
-|+|..|+.+..
T Consensus 285 FFkC~~C~~Rt~ 296 (344)
T PF09332_consen 285 FFKCKDCGNRTI 296 (344)
T ss_dssp EEE-T-TS-EEE
T ss_pred eEECCCCCCeee
Confidence 388999987643
No 341
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=30.44 E-value=40 Score=18.14 Aligned_cols=32 Identities=25% Similarity=0.694 Sum_probs=16.6
Q ss_pred ceecCCCccccccchhHHHHHHhhCCCCCeecCcCcccc
Q psy3500 46 PYKCEYCAYSCTQSSALKIHERKHTGDKPYICQQCRDTF 84 (98)
Q Consensus 46 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 84 (98)
.|.|..|+..+.. +.+... ...|.|..|+..+
T Consensus 112 ~y~C~~C~~~~~~------~rr~~~-~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLR------VRRSNN-VSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCce------EccccC-cceEEcCCCCCEE
Confidence 4667777765432 112111 1347777777554
No 342
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=30.20 E-value=1.2e+02 Score=17.63 Aligned_cols=13 Identities=31% Similarity=0.782 Sum_probs=8.7
Q ss_pred ceecCCCcccccc
Q psy3500 46 PYKCEYCAYSCTQ 58 (98)
Q Consensus 46 ~~~c~~c~~~~~~ 58 (98)
...|++|...+..
T Consensus 68 ~~~CPvCR~~Is~ 80 (193)
T PLN03208 68 PPKCPVCKSDVSE 80 (193)
T ss_pred CCcCCCCCCcCCh
Confidence 4578888766544
No 343
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=30.17 E-value=29 Score=22.45 Aligned_cols=10 Identities=40% Similarity=0.996 Sum_probs=4.5
Q ss_pred CCCCCCCCcc
Q psy3500 2 YHCKTCSTLS 11 (98)
Q Consensus 2 ~~c~~c~~~~ 11 (98)
|.|.+|+.-+
T Consensus 328 ~~c~~~~~e~ 337 (411)
T COG1503 328 YKCPTCGYEN 337 (411)
T ss_pred ecCCCcchhh
Confidence 4445555433
No 344
>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=30.15 E-value=49 Score=18.21 Aligned_cols=17 Identities=18% Similarity=0.350 Sum_probs=12.3
Q ss_pred ceecCCCCCcCCCHHHH
Q psy3500 18 KYTCYACDYHTLMSEDM 34 (98)
Q Consensus 18 ~~~c~~C~~~~~~~~~l 34 (98)
.-+|..|++.|.....+
T Consensus 28 RReC~~C~~RFTTyErv 44 (147)
T TIGR00244 28 RRECLECHERFTTFERA 44 (147)
T ss_pred cccCCccCCccceeeec
Confidence 46788899888765443
No 345
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.10 E-value=44 Score=22.99 Aligned_cols=8 Identities=25% Similarity=0.625 Sum_probs=4.2
Q ss_pred eecCCCCC
Q psy3500 19 YTCYACDY 26 (98)
Q Consensus 19 ~~c~~C~~ 26 (98)
+.|+.||.
T Consensus 581 ~~CP~CGs 588 (623)
T PRK08271 581 KRCPICGS 588 (623)
T ss_pred cCCcCCCC
Confidence 45555553
No 346
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=29.97 E-value=44 Score=18.48 Aligned_cols=17 Identities=18% Similarity=0.323 Sum_probs=11.8
Q ss_pred CceecCCCCCcCCCHHH
Q psy3500 17 YKYTCYACDYHTLMSED 33 (98)
Q Consensus 17 ~~~~c~~C~~~~~~~~~ 33 (98)
..-.|..|+..|.....
T Consensus 27 RRReC~~C~~RFTTfE~ 43 (156)
T COG1327 27 RRRECLECGERFTTFER 43 (156)
T ss_pred hhhcccccccccchhhe
Confidence 34678888888866543
No 347
>PLN02748 tRNA dimethylallyltransferase
Probab=29.94 E-value=47 Score=21.98 Aligned_cols=24 Identities=21% Similarity=0.614 Sum_probs=19.5
Q ss_pred CCeecCcCcc-cccChHHHHHHHhh
Q psy3500 73 KPYICQQCRD-TFSSLYLFRNHLQS 96 (98)
Q Consensus 73 ~~~~C~~C~~-~f~~~~~l~~H~~~ 96 (98)
+.|.|..|++ .+.-..++..|++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 4578999997 78888889888753
No 348
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=29.54 E-value=52 Score=16.53 Aligned_cols=25 Identities=20% Similarity=0.543 Sum_probs=16.1
Q ss_pred CCCCCCCCCccCC--CC-CCceecCCCC
Q psy3500 1 MYHCKTCSTLSRP--NI-SYKYTCYACD 25 (98)
Q Consensus 1 ~~~c~~c~~~~~~--~~-~~~~~c~~C~ 25 (98)
.|.|..||..-.+ .+ ...-.|+.|-
T Consensus 4 ~F~C~~CG~~V~p~~~g~~~RNHCP~CL 31 (92)
T PF12647_consen 4 SFTCVHCGLTVSPLAAGSAHRNHCPSCL 31 (92)
T ss_pred ccCccccCCCcccCCCCCCccCcCcccc
Confidence 4889999987654 22 2445577773
No 349
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=28.95 E-value=24 Score=16.34 Aligned_cols=7 Identities=43% Similarity=1.379 Sum_probs=3.9
Q ss_pred eecCcCc
Q psy3500 75 YICQQCR 81 (98)
Q Consensus 75 ~~C~~C~ 81 (98)
|.|++|+
T Consensus 1 y~C~KCg 7 (64)
T PF09855_consen 1 YKCPKCG 7 (64)
T ss_pred CCCCCCC
Confidence 4566665
No 350
>PLN02436 cellulose synthase A
Probab=28.75 E-value=88 Score=23.28 Aligned_cols=50 Identities=14% Similarity=0.255 Sum_probs=28.3
Q ss_pred CCCCCCCc--cCCCCCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccc
Q psy3500 3 HCKTCSTL--SRPNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCT 57 (98)
Q Consensus 3 ~c~~c~~~--~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~ 57 (98)
.|++||-. ....|+.--.|.+|+...-...- . .- ..+....|+.|...|.
T Consensus 38 iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-e-ye---r~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 38 TCQICGDEIELTVDGEPFVACNECAFPVCRPCY-E-YE---RREGNQACPQCKTRYK 89 (1094)
T ss_pred cccccccccCcCCCCCEEEeeccCCCccccchh-h-hh---hhcCCccCcccCCchh
Confidence 68999964 35667765568888654433221 1 11 1222346777776665
No 351
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=28.55 E-value=33 Score=14.13 Aligned_cols=9 Identities=22% Similarity=0.707 Sum_probs=5.1
Q ss_pred CCCCCCCCC
Q psy3500 1 MYHCKTCST 9 (98)
Q Consensus 1 ~~~c~~c~~ 9 (98)
|..|+.||.
T Consensus 2 ~~~Cp~Cg~ 10 (47)
T PF14690_consen 2 PPRCPHCGS 10 (47)
T ss_pred CccCCCcCC
Confidence 345666664
No 352
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.40 E-value=43 Score=15.42 Aligned_cols=41 Identities=15% Similarity=0.156 Sum_probs=21.6
Q ss_pred CCCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCcccccc
Q psy3500 14 NISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCTQ 58 (98)
Q Consensus 14 ~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~ 58 (98)
.+++++.|+--+..+.....+.. + ..+....|++|+..|..
T Consensus 20 ~~~~~l~C~g~~~p~~HPrV~L~-m---g~~gev~CPYC~t~y~l 60 (62)
T COG4391 20 IGDLPLMCPGPEPPNDHPRVFLD-M---GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred eCCeeEEcCCCCCCCCCCEEEEE-c---CCCCcEecCccccEEEe
Confidence 34566767655444443322111 1 23445788888877653
No 353
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=28.33 E-value=28 Score=13.73 Aligned_cols=7 Identities=29% Similarity=1.317 Sum_probs=1.8
Q ss_pred CCCCCCc
Q psy3500 4 CKTCSTL 10 (98)
Q Consensus 4 c~~c~~~ 10 (98)
|..||..
T Consensus 14 C~~Cg~~ 20 (37)
T PF12172_consen 14 CRDCGRV 20 (37)
T ss_dssp -TTT--E
T ss_pred cCCCCCE
Confidence 4444444
No 354
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=28.31 E-value=35 Score=18.46 Aligned_cols=7 Identities=57% Similarity=1.232 Sum_probs=3.2
Q ss_pred ecCCCcc
Q psy3500 48 KCEYCAY 54 (98)
Q Consensus 48 ~c~~c~~ 54 (98)
.|..||.
T Consensus 125 ~C~ACGa 131 (138)
T PRK03988 125 KCEACGA 131 (138)
T ss_pred EcccCCC
Confidence 4444443
No 355
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=28.24 E-value=38 Score=21.62 Aligned_cols=26 Identities=19% Similarity=0.324 Sum_probs=14.0
Q ss_pred CCCCCCCCccCCCCCCceecCCCCCc
Q psy3500 2 YHCKTCSTLSRPNISYKYTCYACDYH 27 (98)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~c~~C~~~ 27 (98)
+.|..|+......+..+-.|+.|+..
T Consensus 245 ~~C~~c~~~~~~~~~~~~~C~~c~~~ 270 (382)
T PRK04338 245 YYCPKCLYREEVEGLPPEECPVCGGK 270 (382)
T ss_pred EECCCCCcEEEecCCCCCCCCCCCCc
Confidence 45777775443333344457766644
No 356
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=28.18 E-value=34 Score=18.38 Aligned_cols=7 Identities=57% Similarity=1.232 Sum_probs=3.4
Q ss_pred ecCCCcc
Q psy3500 48 KCEYCAY 54 (98)
Q Consensus 48 ~c~~c~~ 54 (98)
.|..||.
T Consensus 120 ~C~ACGa 126 (133)
T TIGR00311 120 KCEACGA 126 (133)
T ss_pred ecccCCC
Confidence 4555553
No 357
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=28.17 E-value=33 Score=15.29 Aligned_cols=16 Identities=13% Similarity=0.279 Sum_probs=7.7
Q ss_pred eecCcCcccccChHHH
Q psy3500 75 YICQQCRDTFSSLYLF 90 (98)
Q Consensus 75 ~~C~~C~~~f~~~~~l 90 (98)
+-|-+||..|.....|
T Consensus 28 ~YC~~Cg~~Y~d~~dL 43 (55)
T PF13821_consen 28 NYCFWCGTKYDDEEDL 43 (55)
T ss_pred ceeeeeCCccCCHHHH
Confidence 3455555555444444
No 358
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=28.07 E-value=69 Score=21.68 Aligned_cols=28 Identities=18% Similarity=0.430 Sum_probs=16.6
Q ss_pred CCCCCCCccCC--------C----CCCceecCCCCCcCCC
Q psy3500 3 HCKTCSTLSRP--------N----ISYKYTCYACDYHTLM 30 (98)
Q Consensus 3 ~c~~c~~~~~~--------~----~~~~~~c~~C~~~~~~ 30 (98)
+|++||..+.. . ....|.|+.|+..+..
T Consensus 202 pCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 202 PCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred cCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCH
Confidence 68888864331 1 1234778888776654
No 359
>KOG1842|consensus
Probab=27.81 E-value=35 Score=22.42 Aligned_cols=22 Identities=23% Similarity=0.615 Sum_probs=18.1
Q ss_pred CeecCcCcccccChHHHHHHHh
Q psy3500 74 PYICQQCRDTFSSLYLFRNHLQ 95 (98)
Q Consensus 74 ~~~C~~C~~~f~~~~~l~~H~~ 95 (98)
.|.|+.|.+.|.....|..|..
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d 36 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLD 36 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHh
Confidence 5888888888888888888864
No 360
>KOG0978|consensus
Probab=27.58 E-value=16 Score=25.21 Aligned_cols=19 Identities=21% Similarity=0.572 Sum_probs=13.2
Q ss_pred CCeecCcCcccccChHHHH
Q psy3500 73 KPYICQQCRDTFSSLYLFR 91 (98)
Q Consensus 73 ~~~~C~~C~~~f~~~~~l~ 91 (98)
|.-+||.|+.+|+....+.
T Consensus 677 RqRKCP~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVHR 695 (698)
T ss_pred hcCCCCCCCCCCCcccccc
Confidence 3457888988888765443
No 361
>KOG2817|consensus
Probab=27.57 E-value=62 Score=20.91 Aligned_cols=16 Identities=19% Similarity=0.590 Sum_probs=10.9
Q ss_pred HhhCCCCCeecCcCcc
Q psy3500 67 RKHTGDKPYICQQCRD 82 (98)
Q Consensus 67 ~~~~~~~~~~C~~C~~ 82 (98)
.+..|...|+||.|..
T Consensus 367 LS~ng~~sfKCPYCP~ 382 (394)
T KOG2817|consen 367 LSKNGSQSFKCPYCPV 382 (394)
T ss_pred HhhCCCeeeeCCCCCc
Confidence 3445566789998864
No 362
>PRK01343 zinc-binding protein; Provisional
Probab=27.13 E-value=41 Score=15.24 Aligned_cols=10 Identities=30% Similarity=0.713 Sum_probs=7.1
Q ss_pred CCCCCCCccC
Q psy3500 3 HCKTCSTLSR 12 (98)
Q Consensus 3 ~c~~c~~~~~ 12 (98)
.|.+||+.+.
T Consensus 11 ~CP~C~k~~~ 20 (57)
T PRK01343 11 PCPECGKPST 20 (57)
T ss_pred cCCCCCCcCc
Confidence 5788887654
No 363
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=27.11 E-value=43 Score=18.60 Aligned_cols=11 Identities=27% Similarity=1.017 Sum_probs=6.8
Q ss_pred ceecCCCCCcC
Q psy3500 18 KYTCYACDYHT 28 (98)
Q Consensus 18 ~~~c~~C~~~~ 28 (98)
.+.|..||...
T Consensus 29 sf~C~~CGyk~ 39 (160)
T smart00709 29 SFECEHCGYRN 39 (160)
T ss_pred EEECCCCCCcc
Confidence 46677776544
No 364
>KOG1994|consensus
Probab=27.06 E-value=39 Score=20.08 Aligned_cols=21 Identities=19% Similarity=0.376 Sum_probs=17.5
Q ss_pred CCeecCcCcccccChHHHHHH
Q psy3500 73 KPYICQQCRDTFSSLYLFRNH 93 (98)
Q Consensus 73 ~~~~C~~C~~~f~~~~~l~~H 93 (98)
--|-|-.||-.|....+|..|
T Consensus 238 eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 238 EHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred cceEEEEeccccCCHHHHHHh
Confidence 358899999999988888776
No 365
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.99 E-value=29 Score=15.08 Aligned_cols=12 Identities=42% Similarity=0.841 Sum_probs=6.2
Q ss_pred ecCcCcccccCh
Q psy3500 76 ICQQCRDTFSSL 87 (98)
Q Consensus 76 ~C~~C~~~f~~~ 87 (98)
.|+.|++-|...
T Consensus 14 ICpvCqRPFsWR 25 (54)
T COG4338 14 ICPVCQRPFSWR 25 (54)
T ss_pred hhhhhcCchHHH
Confidence 355555555443
No 366
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=26.85 E-value=65 Score=14.72 Aligned_cols=13 Identities=15% Similarity=0.503 Sum_probs=7.4
Q ss_pred ceecCCCcccccc
Q psy3500 46 PYKCEYCAYSCTQ 58 (98)
Q Consensus 46 ~~~c~~c~~~~~~ 58 (98)
...|..|+.....
T Consensus 30 ~V~C~~Cg~~L~~ 42 (59)
T PRK00415 30 VVRCLVCGKTLAE 42 (59)
T ss_pred EEECcccCCCccc
Confidence 4566666665544
No 367
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=26.81 E-value=66 Score=13.68 Aligned_cols=20 Identities=30% Similarity=0.946 Sum_probs=11.8
Q ss_pred CCCCCCccCCCCCCceecCCCC
Q psy3500 4 CKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
|+-|+.. +.....|+|.+|.
T Consensus 3 Cd~C~~~--pI~G~RykC~~C~ 22 (45)
T cd02344 3 CDGCQMF--PINGPRFKCRNCD 22 (45)
T ss_pred CCCCCCC--CCccCeEECCCCC
Confidence 5555532 3334678888886
No 368
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=26.80 E-value=67 Score=19.75 Aligned_cols=24 Identities=21% Similarity=0.502 Sum_probs=14.6
Q ss_pred CCCCCC-ccCCCCCCceecCCCCCc
Q psy3500 4 CKTCST-LSRPNISYKYTCYACDYH 27 (98)
Q Consensus 4 c~~c~~-~~~~~~~~~~~c~~C~~~ 27 (98)
|..||. +.-..++....|+.|+..
T Consensus 114 Cg~CG~~~~~~~~g~~~~C~~cg~~ 138 (279)
T COG2816 114 CGRCGTKTYPREGGWARVCPKCGHE 138 (279)
T ss_pred CCCCCCcCccccCceeeeCCCCCCc
Confidence 455553 333455667788888754
No 369
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=26.64 E-value=31 Score=18.42 Aligned_cols=22 Identities=23% Similarity=0.486 Sum_probs=9.2
Q ss_pred CCCCccCCCCCCceecCCCCCc
Q psy3500 6 TCSTLSRPNISYKYTCYACDYH 27 (98)
Q Consensus 6 ~c~~~~~~~~~~~~~c~~C~~~ 27 (98)
.|++--...++-.|.|..|+..
T Consensus 25 ~C~kKv~~~~~~~y~C~~C~~~ 46 (146)
T PF08646_consen 25 KCNKKVTENGDGSYRCEKCNKT 46 (146)
T ss_dssp TTS-B-EEETTTEEEETTTTEE
T ss_pred cCCCEeecCCCcEEECCCCCCc
Confidence 4554333333334555555544
No 370
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=26.58 E-value=1e+02 Score=22.89 Aligned_cols=50 Identities=14% Similarity=0.312 Sum_probs=29.5
Q ss_pred CCCCCCCc--cCCCCCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccc
Q psy3500 3 HCKTCSTL--SRPNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCT 57 (98)
Q Consensus 3 ~c~~c~~~--~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~ 57 (98)
.|++||-. ...+|+.--.|.+|+...-.... . . -..+....|+.|+..|.
T Consensus 17 ~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy-e-y---e~~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 17 TCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCY-E-Y---ERSEGNQCCPQCNTRYK 68 (1044)
T ss_pred hhhccccccCcCCCCCEEEEeccCCCccccchh-h-h---hhhcCCccCCccCCchh
Confidence 68999963 45677765668888755433221 1 0 11223356888876665
No 371
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=26.51 E-value=89 Score=16.00 Aligned_cols=13 Identities=15% Similarity=0.659 Sum_probs=7.0
Q ss_pred eecCcCcccccCh
Q psy3500 75 YICQQCRDTFSSL 87 (98)
Q Consensus 75 ~~C~~C~~~f~~~ 87 (98)
+.|+.||..+...
T Consensus 32 ~~C~~CGe~~~~~ 44 (127)
T TIGR03830 32 WYCPACGEELLDP 44 (127)
T ss_pred eECCCCCCEEEcH
Confidence 4566666555443
No 372
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=26.48 E-value=77 Score=15.82 Aligned_cols=16 Identities=13% Similarity=0.345 Sum_probs=8.6
Q ss_pred eecCcCcccccChHHH
Q psy3500 75 YICQQCRDTFSSLYLF 90 (98)
Q Consensus 75 ~~C~~C~~~f~~~~~l 90 (98)
..|+.||..+......
T Consensus 36 ~~C~~CGe~y~~dev~ 51 (89)
T TIGR03829 36 ISCSHCGMEYQDDTTV 51 (89)
T ss_pred ccccCCCcEeecHHHH
Confidence 4566666655554433
No 373
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=26.47 E-value=85 Score=20.11 Aligned_cols=72 Identities=22% Similarity=0.394 Sum_probs=39.3
Q ss_pred eecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCc----cccccchhHHHHHHhhCCCCCeecCc--Cc----ccccChH
Q psy3500 19 YTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCA----YSCTQSSALKIHERKHTGDKPYICQQ--CR----DTFSSLY 88 (98)
Q Consensus 19 ~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~----~~~~~~~~l~~h~~~~~~~~~~~C~~--C~----~~f~~~~ 88 (98)
-.|..|...|-..+.|..|++... ++-+.|++-+ ..|..-..|..|.+ ..-|-|.. |. ..|....
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~----~~hy~ct~qtc~~~k~~vf~~~~ 295 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFR----NAHYCCTFQTCRVGKCYVFPYHT 295 (493)
T ss_pred chhhhccceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhh----cCceEEEEEEEecCcEEEeccHH
Confidence 357778877877788888876322 2234444433 23333344444433 22354421 32 3577778
Q ss_pred HHHHHHh
Q psy3500 89 LFRNHLQ 95 (98)
Q Consensus 89 ~l~~H~~ 95 (98)
.|..|+.
T Consensus 296 el~~h~~ 302 (493)
T COG5236 296 ELLEHLT 302 (493)
T ss_pred HHHHHHH
Confidence 8888763
No 374
>KOG3183|consensus
Probab=26.42 E-value=27 Score=20.82 Aligned_cols=11 Identities=27% Similarity=0.812 Sum_probs=8.5
Q ss_pred CCCCCCCCCcc
Q psy3500 1 MYHCKTCSTLS 11 (98)
Q Consensus 1 ~~~c~~c~~~~ 11 (98)
||+|+-|+.-|
T Consensus 23 Pf~Cd~C~~~F 33 (250)
T KOG3183|consen 23 PFKCDGCSGIF 33 (250)
T ss_pred ceeeCCccchh
Confidence 78899888644
No 375
>KOG3277|consensus
Probab=26.29 E-value=47 Score=18.45 Aligned_cols=36 Identities=22% Similarity=0.472 Sum_probs=20.0
Q ss_pred CCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCcc
Q psy3500 16 SYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAY 54 (98)
Q Consensus 16 ~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~ 54 (98)
.+.|+|.+|+.+... .+.. +.-+.|-.-..|+.|..
T Consensus 77 ~l~yTCkvCntRs~k--tisk-~AY~~GvVivqC~gC~~ 112 (165)
T KOG3277|consen 77 QLAYTCKVCNTRSTK--TISK-QAYEKGVVIVQCPGCKN 112 (165)
T ss_pred EEEEEeeccCCcccc--ccCh-hhhhCceEEEECCCCcc
Confidence 345899999755331 1111 12344555677887764
No 376
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=25.93 E-value=31 Score=15.22 Aligned_cols=9 Identities=22% Similarity=0.814 Sum_probs=5.3
Q ss_pred ecCcCcccc
Q psy3500 76 ICQQCRDTF 84 (98)
Q Consensus 76 ~C~~C~~~f 84 (98)
.|+.||..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 466676544
No 377
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=25.69 E-value=33 Score=15.48 Aligned_cols=11 Identities=18% Similarity=0.455 Sum_probs=4.4
Q ss_pred CCCCCCCccCC
Q psy3500 3 HCKTCSTLSRP 13 (98)
Q Consensus 3 ~c~~c~~~~~~ 13 (98)
.|++||+....
T Consensus 4 ~CP~C~k~~~~ 14 (57)
T PF03884_consen 4 KCPICGKPVEW 14 (57)
T ss_dssp E-TTT--EEE-
T ss_pred cCCCCCCeecc
Confidence 47777776554
No 378
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=25.61 E-value=86 Score=14.66 Aligned_cols=20 Identities=20% Similarity=0.436 Sum_probs=12.1
Q ss_pred CCCCccCCCCCCceecCCCCC
Q psy3500 6 TCSTLSRPNISYKYTCYACDY 26 (98)
Q Consensus 6 ~c~~~~~~~~~~~~~c~~C~~ 26 (98)
.|+..+.. ++.-|.|..|..
T Consensus 2 ~C~~~~~~-~~~~y~C~tC~~ 21 (71)
T smart00396 2 VCTYKFTG-GEVIYRCKTCGL 21 (71)
T ss_pred CCCCccCC-CCEEEECcCCCC
Confidence 46666554 344578877753
No 379
>PLN02189 cellulose synthase
Probab=25.15 E-value=1.1e+02 Score=22.67 Aligned_cols=50 Identities=14% Similarity=0.282 Sum_probs=28.0
Q ss_pred CCCCCCCc--cCCCCCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccc
Q psy3500 3 HCKTCSTL--SRPNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCT 57 (98)
Q Consensus 3 ~c~~c~~~--~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~ 57 (98)
.|++||-. ...+|+.--.|.+|+...-...- ..- ..+....|+.|+..|.
T Consensus 36 ~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy--eye---r~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 36 VCEICGDEIGLTVDGDLFVACNECGFPVCRPCY--EYE---RREGTQNCPQCKTRYK 87 (1040)
T ss_pred cccccccccCcCCCCCEEEeeccCCCccccchh--hhh---hhcCCccCcccCCchh
Confidence 68899964 34666655568877654433221 111 1223356777776665
No 380
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=25.00 E-value=78 Score=14.29 Aligned_cols=7 Identities=43% Similarity=1.379 Sum_probs=3.5
Q ss_pred eecCCCc
Q psy3500 47 YKCEYCA 53 (98)
Q Consensus 47 ~~c~~c~ 53 (98)
|.|+.|.
T Consensus 32 YmC~eC~ 38 (56)
T PF09963_consen 32 YMCDECK 38 (56)
T ss_pred eeChhHH
Confidence 5555543
No 381
>KOG2846|consensus
Probab=24.86 E-value=48 Score=20.79 Aligned_cols=22 Identities=23% Similarity=0.449 Sum_probs=15.4
Q ss_pred CCCCccCCCCC--------CceecCCCCCc
Q psy3500 6 TCSTLSRPNIS--------YKYTCYACDYH 27 (98)
Q Consensus 6 ~c~~~~~~~~~--------~~~~c~~C~~~ 27 (98)
+|+.++.|+|- ..|.|..|...
T Consensus 222 IC~~C~~HNGla~~ee~~yi~F~C~~Cn~L 251 (328)
T KOG2846|consen 222 ICSQCHHHNGLARKEEYEYITFRCPHCNAL 251 (328)
T ss_pred cchhhccccCcCChhhcCceEEECcccccc
Confidence 67788877773 24788888754
No 382
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=24.77 E-value=49 Score=14.22 Aligned_cols=11 Identities=18% Similarity=0.480 Sum_probs=7.1
Q ss_pred CCCCCCccCCC
Q psy3500 4 CKTCSTLSRPN 14 (98)
Q Consensus 4 c~~c~~~~~~~ 14 (98)
|+.||..|.=.
T Consensus 1 CP~Cg~~f~C~ 11 (50)
T PF14375_consen 1 CPRCGAPFECG 11 (50)
T ss_pred CCCCCCcCCCC
Confidence 56777776643
No 383
>PRK02935 hypothetical protein; Provisional
Probab=24.75 E-value=48 Score=17.12 Aligned_cols=14 Identities=21% Similarity=0.328 Sum_probs=8.0
Q ss_pred eecCCCccccccch
Q psy3500 47 YKCEYCAYSCTQSS 60 (98)
Q Consensus 47 ~~c~~c~~~~~~~~ 60 (98)
..|..|+....-..
T Consensus 87 D~CM~C~~PLTLd~ 100 (110)
T PRK02935 87 DACMHCNQPLTLDR 100 (110)
T ss_pred eecCcCCCcCCcCc
Confidence 46666766554443
No 384
>KOG2636|consensus
Probab=24.63 E-value=66 Score=21.27 Aligned_cols=27 Identities=26% Similarity=0.498 Sum_probs=18.2
Q ss_pred HhhCCCCCeecCcCc-ccccChHHHHHH
Q psy3500 67 RKHTGDKPYICQQCR-DTFSSLYLFRNH 93 (98)
Q Consensus 67 ~~~~~~~~~~C~~C~-~~f~~~~~l~~H 93 (98)
+.|-....|.|..|| .++.-...+.+|
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRH 421 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHH
Confidence 456667778888888 555555556555
No 385
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=24.54 E-value=61 Score=15.01 Aligned_cols=6 Identities=33% Similarity=1.010 Sum_probs=3.0
Q ss_pred cCCCCC
Q psy3500 21 CYACDY 26 (98)
Q Consensus 21 c~~C~~ 26 (98)
|+.|+.
T Consensus 21 CP~Cgs 26 (64)
T COG2093 21 CPVCGS 26 (64)
T ss_pred CCCCCC
Confidence 555543
No 386
>KOG1729|consensus
Probab=24.48 E-value=6.7 Score=23.88 Aligned_cols=7 Identities=29% Similarity=1.065 Sum_probs=3.2
Q ss_pred ecCCCCC
Q psy3500 20 TCYACDY 26 (98)
Q Consensus 20 ~c~~C~~ 26 (98)
.|..|+.
T Consensus 170 ~C~~C~~ 176 (288)
T KOG1729|consen 170 ECMVCGC 176 (288)
T ss_pred ecccCCC
Confidence 3444444
No 387
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=24.45 E-value=58 Score=18.71 Aligned_cols=10 Identities=20% Similarity=0.557 Sum_probs=4.4
Q ss_pred ceecCCCCCc
Q psy3500 18 KYTCYACDYH 27 (98)
Q Consensus 18 ~~~c~~C~~~ 27 (98)
...|+.|+.+
T Consensus 165 ~l~Cp~Cg~t 174 (188)
T COG1096 165 MLKCPNCGNT 174 (188)
T ss_pred EEECCCCCCE
Confidence 3344444443
No 388
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.27 E-value=87 Score=16.86 Aligned_cols=24 Identities=17% Similarity=0.246 Sum_probs=13.2
Q ss_pred cCCCHHHHHHHHHHhcCCCceecCCCcc
Q psy3500 27 HTLMSEDMKKHMRKHTGEKPYKCEYCAY 54 (98)
Q Consensus 27 ~~~~~~~l~~h~~~h~~~~~~~c~~c~~ 54 (98)
+|.....+.++. ......|++|+.
T Consensus 17 WF~ssaDfd~Q~----~rgLv~CPvCgs 40 (142)
T COG5319 17 WFGSSADFDRQR----ERGLVTCPVCGS 40 (142)
T ss_pred cccCchhHHHHH----HcCceeCCCCCc
Confidence 466666655442 233466777764
No 389
>KOG4317|consensus
Probab=24.23 E-value=18 Score=22.56 Aligned_cols=10 Identities=40% Similarity=0.932 Sum_probs=5.9
Q ss_pred eecCCCCCcC
Q psy3500 19 YTCYACDYHT 28 (98)
Q Consensus 19 ~~c~~C~~~~ 28 (98)
|+|+-|+-.+
T Consensus 20 YtCPRCn~~Y 29 (383)
T KOG4317|consen 20 YTCPRCNLLY 29 (383)
T ss_pred ccCCCCCccc
Confidence 6666665444
No 390
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=24.12 E-value=1.1e+02 Score=16.84 Aligned_cols=26 Identities=12% Similarity=0.198 Sum_probs=13.6
Q ss_pred cCCCHHHHHHHHHHhcCCCceecCCCcccc
Q psy3500 27 HTLMSEDMKKHMRKHTGEKPYKCEYCAYSC 56 (98)
Q Consensus 27 ~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~ 56 (98)
+|.+...+..+. ......|++||..-
T Consensus 17 WF~ss~~fd~Q~----~~glv~CP~Cgs~~ 42 (148)
T PF06676_consen 17 WFRSSAAFDRQQ----ARGLVSCPVCGSTE 42 (148)
T ss_pred ecCCHHHHHHHH----HcCCccCCCCCCCe
Confidence 455555555443 22345677776533
No 391
>COG4640 Predicted membrane protein [Function unknown]
Probab=24.02 E-value=87 Score=20.47 Aligned_cols=30 Identities=13% Similarity=0.396 Sum_probs=18.6
Q ss_pred CCCCCCccCCCCCCceecCCCCCcCCCHHHHHH
Q psy3500 4 CKTCSTLSRPNISYKYTCYACDYHTLMSEDMKK 36 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~~~~~~~~~l~~ 36 (98)
|+-||.. ..+=.+.|+.||..|.....+..
T Consensus 4 C~kcG~q---k~Ed~~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 4 CPKCGSQ---KAEDDVQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred ccccccc---cccccccccccCCcCCchhhhhh
Confidence 5555543 33333449999988877766554
No 392
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=23.52 E-value=42 Score=17.01 Aligned_cols=13 Identities=31% Similarity=0.695 Sum_probs=9.6
Q ss_pred CCCeecCcCcccc
Q psy3500 72 DKPYICQQCRDTF 84 (98)
Q Consensus 72 ~~~~~C~~C~~~f 84 (98)
.+..+|..||..|
T Consensus 86 ~r~~rC~nCG~~f 98 (98)
T PF10164_consen 86 MRERRCSNCGATF 98 (98)
T ss_pred cCccccCCCCccC
Confidence 4567888888765
No 393
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=23.23 E-value=77 Score=13.20 Aligned_cols=11 Identities=18% Similarity=0.594 Sum_probs=6.4
Q ss_pred ceecCCCCCcC
Q psy3500 18 KYTCYACDYHT 28 (98)
Q Consensus 18 ~~~c~~C~~~~ 28 (98)
.+.|..|+..+
T Consensus 11 l~~CL~C~~~~ 21 (50)
T smart00290 11 LWLCLTCGQVG 21 (50)
T ss_pred eEEecCCCCcc
Confidence 55666666444
No 394
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=23.17 E-value=82 Score=22.18 Aligned_cols=8 Identities=38% Similarity=1.074 Sum_probs=4.8
Q ss_pred eecCCCCC
Q psy3500 19 YTCYACDY 26 (98)
Q Consensus 19 ~~c~~C~~ 26 (98)
+.|+.||.
T Consensus 660 ~~CP~CG~ 667 (711)
T PRK09263 660 FTCPKCGN 667 (711)
T ss_pred CcCcCCCC
Confidence 55666654
No 395
>KOG0696|consensus
Probab=23.10 E-value=21 Score=23.55 Aligned_cols=46 Identities=22% Similarity=0.377 Sum_probs=20.0
Q ss_pred HHHHHHhcCCCceecCCCccccccchhHHHHH-HhhCCCCCeecCcCc
Q psy3500 35 KKHMRKHTGEKPYKCEYCAYSCTQSSALKIHE-RKHTGDKPYICQQCR 81 (98)
Q Consensus 35 ~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~-~~~~~~~~~~C~~C~ 81 (98)
..|.+.|. -..|.|+.-.+.+.....-..|. ..++-..|--|.+||
T Consensus 82 vvHkrChe-fVtF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCG 128 (683)
T KOG0696|consen 82 VVHKRCHE-FVTFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCG 128 (683)
T ss_pred hhhhhhcc-eEEEECCCCCCCCCCCCcccccceeeeecCCCchhhhHH
Confidence 34555543 23455655555554444333332 233333343444444
No 396
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=23.07 E-value=53 Score=18.96 Aligned_cols=26 Identities=19% Similarity=0.352 Sum_probs=14.7
Q ss_pred CCCCCCCCc-------cCCCCCCceecCCCCCc
Q psy3500 2 YHCKTCSTL-------SRPNISYKYTCYACDYH 27 (98)
Q Consensus 2 ~~c~~c~~~-------~~~~~~~~~~c~~C~~~ 27 (98)
+.|-+||.- +.+..-+--.|+.|++.
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~v 33 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKV 33 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCc
Confidence 467788853 22333344567777754
No 397
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=23.00 E-value=43 Score=13.13 Aligned_cols=6 Identities=33% Similarity=1.359 Sum_probs=2.4
Q ss_pred CCCCCC
Q psy3500 4 CKTCST 9 (98)
Q Consensus 4 c~~c~~ 9 (98)
|..||+
T Consensus 6 C~~CGe 11 (36)
T PF01258_consen 6 CEDCGE 11 (36)
T ss_dssp -TTTSS
T ss_pred ccccCC
Confidence 445554
No 398
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=22.97 E-value=57 Score=17.06 Aligned_cols=19 Identities=21% Similarity=0.614 Sum_probs=9.0
Q ss_pred CCCCCCccCCCCCCceecCCCC
Q psy3500 4 CKTCSTLSRPNISYKYTCYACD 25 (98)
Q Consensus 4 c~~c~~~~~~~~~~~~~c~~C~ 25 (98)
|+.||.-..- -.+.|+.|+
T Consensus 1 CPvCg~~l~v---t~l~C~~C~ 19 (113)
T PF09862_consen 1 CPVCGGELVV---TRLKCPSCG 19 (113)
T ss_pred CCCCCCceEE---EEEEcCCCC
Confidence 5666643221 234555555
No 399
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=22.94 E-value=7.6 Score=17.04 Aligned_cols=12 Identities=25% Similarity=0.791 Sum_probs=6.8
Q ss_pred ceecCCCCCcCC
Q psy3500 18 KYTCYACDYHTL 29 (98)
Q Consensus 18 ~~~c~~C~~~~~ 29 (98)
.|.|..|..+++
T Consensus 7 ry~CDLCn~~~p 18 (57)
T PF14445_consen 7 RYSCDLCNSSHP 18 (57)
T ss_pred hHhHHhhcccCc
Confidence 356666665554
No 400
>KOG0782|consensus
Probab=22.92 E-value=17 Score=24.76 Aligned_cols=50 Identities=18% Similarity=0.393 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCCceecCCCccccccchhHHHHHHhhCCC-CCeecCcCcccccChH
Q psy3500 33 DMKKHMRKHTGEKPYKCEYCAYSCTQSSALKIHERKHTGD-KPYICQQCRDTFSSLY 88 (98)
Q Consensus 33 ~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~-~~~~C~~C~~~f~~~~ 88 (98)
.+.+|.=+|.....-.|..|+++|...-.+ |..+ ....|.+|...|-.+.
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQKf~F------hsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQKFFF------HSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhheee------ccccEEEEEehHHHHHhhcch
Confidence 455555555555556677777777654332 2211 2356777776665443
No 401
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=22.79 E-value=26 Score=15.70 Aligned_cols=8 Identities=38% Similarity=1.410 Sum_probs=4.2
Q ss_pred CeecCcCc
Q psy3500 74 PYICQQCR 81 (98)
Q Consensus 74 ~~~C~~C~ 81 (98)
|.-|+.|.
T Consensus 28 PlyCpKCK 35 (55)
T PF14205_consen 28 PLYCPKCK 35 (55)
T ss_pred cccCCCCC
Confidence 44555554
No 402
>KOG2703|consensus
Probab=22.65 E-value=34 Score=22.15 Aligned_cols=10 Identities=20% Similarity=0.806 Sum_probs=7.9
Q ss_pred CCCCCCCCCc
Q psy3500 1 MYHCKTCSTL 10 (98)
Q Consensus 1 ~~~c~~c~~~ 10 (98)
.|+|++||.-
T Consensus 68 SF~CpHCG~k 77 (460)
T KOG2703|consen 68 SFECPHCGHK 77 (460)
T ss_pred EeecCccCCc
Confidence 4899999963
No 403
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=22.64 E-value=1.2e+02 Score=16.89 Aligned_cols=12 Identities=17% Similarity=0.650 Sum_probs=6.5
Q ss_pred eecCCCcccccc
Q psy3500 47 YKCEYCAYSCTQ 58 (98)
Q Consensus 47 ~~c~~c~~~~~~ 58 (98)
..|..|++.+..
T Consensus 106 ~~C~~C~~~~~~ 117 (178)
T PF02146_consen 106 LRCSKCGKEYDR 117 (178)
T ss_dssp EEETTTSBEEEG
T ss_pred eeecCCCccccc
Confidence 455666655543
No 404
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=22.46 E-value=40 Score=19.82 Aligned_cols=12 Identities=17% Similarity=0.263 Sum_probs=7.9
Q ss_pred eecCCCcccccc
Q psy3500 47 YKCEYCAYSCTQ 58 (98)
Q Consensus 47 ~~c~~c~~~~~~ 58 (98)
..|+.||..+..
T Consensus 36 ~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 36 TICPKCGRYRIG 47 (236)
T ss_pred eECCCCCCEECC
Confidence 568888865543
No 405
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=22.44 E-value=78 Score=19.02 Aligned_cols=24 Identities=17% Similarity=0.510 Sum_probs=14.3
Q ss_pred CCCCCCccC-CCCCCceecCCCCCc
Q psy3500 4 CKTCSTLSR-PNISYKYTCYACDYH 27 (98)
Q Consensus 4 c~~c~~~~~-~~~~~~~~c~~C~~~ 27 (98)
|..||.-.. ..++....|+.|+..
T Consensus 102 C~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 102 CGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred ccccCCCCeecCCceeEECCCCCCE
Confidence 667776432 334555678888744
No 406
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=22.29 E-value=39 Score=19.17 Aligned_cols=13 Identities=15% Similarity=0.511 Sum_probs=8.7
Q ss_pred CceecCCCCCcCC
Q psy3500 17 YKYTCYACDYHTL 29 (98)
Q Consensus 17 ~~~~c~~C~~~~~ 29 (98)
..+.|.-|.+.|.
T Consensus 138 w~~rC~GC~~~f~ 150 (177)
T COG1439 138 WRLRCHGCKRIFP 150 (177)
T ss_pred eeEEEecCceecC
Confidence 3467777777765
No 407
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=22.27 E-value=74 Score=22.99 Aligned_cols=26 Identities=15% Similarity=0.346 Sum_probs=12.0
Q ss_pred CCCCCCccCCC----CCCceecCCCCCcCC
Q psy3500 4 CKTCSTLSRPN----ISYKYTCYACDYHTL 29 (98)
Q Consensus 4 c~~c~~~~~~~----~~~~~~c~~C~~~~~ 29 (98)
|..|++-|... +..++.|.-||..|-
T Consensus 463 C~~C~kkFfSlsK~L~~RKHHCRkCGrVFC 492 (1374)
T PTZ00303 463 CPSCGRAFISLSRPLGTRAHHCRSCGIRLC 492 (1374)
T ss_pred ccCcCCcccccccccccccccccCCccccC
Confidence 55555555321 123444555555443
No 408
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=22.24 E-value=42 Score=22.58 Aligned_cols=8 Identities=38% Similarity=0.808 Sum_probs=2.4
Q ss_pred eecCCCcc
Q psy3500 47 YKCEYCAY 54 (98)
Q Consensus 47 ~~c~~c~~ 54 (98)
..|+.||.
T Consensus 505 ~~CP~CGs 512 (546)
T PF13597_consen 505 DKCPKCGS 512 (546)
T ss_dssp EE-CCC--
T ss_pred CCCCCCCC
Confidence 44555553
No 409
>TIGR00320 dfx_rbo desulfoferrodoxin. This protein is described in some articles as rubredoxin oxidoreductase (rbo), and its gene shares an operon with the rubredoxin gene in Desulfovibrio vulgaris Hildenborough.
Probab=21.97 E-value=37 Score=17.99 Aligned_cols=10 Identities=30% Similarity=1.175 Sum_probs=7.8
Q ss_pred CCCCCCCCcc
Q psy3500 2 YHCKTCSTLS 11 (98)
Q Consensus 2 ~~c~~c~~~~ 11 (98)
|+|+.||...
T Consensus 8 YkC~~CGniv 17 (125)
T TIGR00320 8 YKCEVCGNIV 17 (125)
T ss_pred EECCCCCcEE
Confidence 7899999754
No 410
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.83 E-value=59 Score=14.98 Aligned_cols=9 Identities=33% Similarity=0.892 Sum_probs=4.9
Q ss_pred ceecCCCcc
Q psy3500 46 PYKCEYCAY 54 (98)
Q Consensus 46 ~~~c~~c~~ 54 (98)
.|-|+.|..
T Consensus 31 tymC~eC~~ 39 (68)
T COG4896 31 TYMCPECEH 39 (68)
T ss_pred eEechhhHh
Confidence 356666543
No 411
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=21.67 E-value=48 Score=24.20 Aligned_cols=9 Identities=22% Similarity=0.862 Sum_probs=4.1
Q ss_pred ceecCCCCC
Q psy3500 18 KYTCYACDY 26 (98)
Q Consensus 18 ~~~c~~C~~ 26 (98)
.|+|..|++
T Consensus 821 ~~~~~~~~~ 829 (1006)
T PRK12775 821 QWRCDDCGK 829 (1006)
T ss_pred eeehhhhcc
Confidence 344444443
No 412
>CHL00112 rpl28 ribosomal protein L28; Provisional
Probab=21.47 E-value=41 Score=15.53 Aligned_cols=8 Identities=13% Similarity=0.426 Sum_probs=5.3
Q ss_pred CCCCCCCc
Q psy3500 3 HCKTCSTL 10 (98)
Q Consensus 3 ~c~~c~~~ 10 (98)
.|+.||+.
T Consensus 4 ~C~i~GK~ 11 (63)
T CHL00112 4 KCQLTGKK 11 (63)
T ss_pred eeccCCCc
Confidence 57777764
No 413
>PF12907 zf-met2: Zinc-binding
Probab=21.36 E-value=62 Score=13.45 Aligned_cols=20 Identities=35% Similarity=0.723 Sum_probs=10.7
Q ss_pred eecCcCccccc---ChHHHHHHH
Q psy3500 75 YICQQCRDTFS---SLYLFRNHL 94 (98)
Q Consensus 75 ~~C~~C~~~f~---~~~~l~~H~ 94 (98)
+.|..|..+|. ....|..|-
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~ 24 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHA 24 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHH
Confidence 45666665443 345566654
No 414
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=21.36 E-value=53 Score=18.95 Aligned_cols=11 Identities=36% Similarity=0.748 Sum_probs=6.8
Q ss_pred ceecCCCCCcC
Q psy3500 18 KYTCYACDYHT 28 (98)
Q Consensus 18 ~~~c~~C~~~~ 28 (98)
...|..||...
T Consensus 119 ~l~C~aCGa~~ 129 (201)
T PRK12336 119 MLRCDACGAHR 129 (201)
T ss_pred EEEcccCCCCc
Confidence 45677777543
No 415
>PF03691 UPF0167: Uncharacterised protein family (UPF0167); InterPro: IPR005363 The proteins in this family are about 200 amino acids long and each contain 3 CXXC motifs.
Probab=21.29 E-value=53 Score=18.65 Aligned_cols=22 Identities=23% Similarity=0.623 Sum_probs=12.5
Q ss_pred CCCCCCCccC--------CCCCCceecCCC
Q psy3500 3 HCKTCSTLSR--------PNISYKYTCYAC 24 (98)
Q Consensus 3 ~c~~c~~~~~--------~~~~~~~~c~~C 24 (98)
+|+.||+... ...+..+.|+.|
T Consensus 26 ~C~cCgk~~~~~Y~~~~Y~~~dv~~lCPwC 55 (176)
T PF03691_consen 26 VCDCCGKARGYYYTGPFYSEEDVEYLCPWC 55 (176)
T ss_pred CcCCCCCCceeEecCCceecCCccccCHhH
Confidence 5888886421 223345666666
No 416
>PLN02195 cellulose synthase A
Probab=20.97 E-value=1.6e+02 Score=21.86 Aligned_cols=50 Identities=20% Similarity=0.266 Sum_probs=29.7
Q ss_pred CCCCCCC--ccCCCCCCceecCCCCCcCCCHHHHHHHHHHhcCCCceecCCCccccc
Q psy3500 3 HCKTCST--LSRPNISYKYTCYACDYHTLMSEDMKKHMRKHTGEKPYKCEYCAYSCT 57 (98)
Q Consensus 3 ~c~~c~~--~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~~~ 57 (98)
.|++||. ....+|+.--.|.+|+...-...- .. -..+....|++|+..|.
T Consensus 8 ~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCy--ey---er~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 8 ICATCGEEVGVDSNGEAFVACHECSYPLCKACL--EY---EIKEGRKVCLRCGGPYD 59 (977)
T ss_pred cceecccccCcCCCCCeEEEeccCCCccccchh--hh---hhhcCCccCCccCCccc
Confidence 5899996 345667755558888754433321 11 11233457888887776
No 417
>PLN03239 histone acetyltransferase; Provisional
Probab=20.91 E-value=91 Score=19.92 Aligned_cols=24 Identities=17% Similarity=0.228 Sum_probs=20.5
Q ss_pred CCCeecCcCcccccChHHHHHHHh
Q psy3500 72 DKPYICQQCRDTFSSLYLFRNHLQ 95 (98)
Q Consensus 72 ~~~~~C~~C~~~f~~~~~l~~H~~ 95 (98)
+.-|.|..|.+-|.....+.+|+.
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHH
Confidence 456999999999999999999875
No 418
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.91 E-value=72 Score=22.22 Aligned_cols=9 Identities=22% Similarity=0.940 Sum_probs=4.5
Q ss_pred ceecCCCcc
Q psy3500 46 PYKCEYCAY 54 (98)
Q Consensus 46 ~~~c~~c~~ 54 (98)
+..|+.|+.
T Consensus 422 p~~Cp~Cgs 430 (665)
T PRK14873 422 DWRCPRCGS 430 (665)
T ss_pred CccCCCCcC
Confidence 345555554
No 419
>KOG4727|consensus
Probab=20.52 E-value=76 Score=18.04 Aligned_cols=21 Identities=24% Similarity=0.558 Sum_probs=17.4
Q ss_pred CeecCcCcccccChHHHHHHH
Q psy3500 74 PYICQQCRDTFSSLYLFRNHL 94 (98)
Q Consensus 74 ~~~C~~C~~~f~~~~~l~~H~ 94 (98)
.|-|..|+-.+....++..|+
T Consensus 75 GyyCdVCdcvvKDSinflDHi 95 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHI 95 (193)
T ss_pred ceeeeecceeehhhHHHHHHh
Confidence 589999999998888777764
No 420
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=20.24 E-value=79 Score=12.21 Aligned_cols=8 Identities=50% Similarity=1.468 Sum_probs=4.7
Q ss_pred ceecCCCC
Q psy3500 18 KYTCYACD 25 (98)
Q Consensus 18 ~~~c~~C~ 25 (98)
.|.|..|+
T Consensus 16 ~~~C~~C~ 23 (32)
T PF13842_consen 16 RYMCSKCD 23 (32)
T ss_pred EEEccCCC
Confidence 45666664
No 421
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=20.15 E-value=1e+02 Score=13.40 Aligned_cols=10 Identities=30% Similarity=0.780 Sum_probs=5.1
Q ss_pred CCCCCCCCcc
Q psy3500 2 YHCKTCSTLS 11 (98)
Q Consensus 2 ~~c~~c~~~~ 11 (98)
..|..|+...
T Consensus 4 ~~C~~C~~~~ 13 (52)
T smart00401 4 RSCSNCGTTE 13 (52)
T ss_pred CCcCCCCCCC
Confidence 3456666433
Done!