Query psy8831
Match_columns 88
No_of_seqs 118 out of 763
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 20:17:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8831.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8831hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00202 ZnF_GATA Zinc finger D 99.7 6.3E-18 1.4E-22 101.8 3.6 43 19-61 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.7 3.8E-17 8.3E-22 97.5 3.6 45 16-60 2-48 (52)
3 PF00320 GATA: GATA zinc finge 99.6 1.2E-16 2.6E-21 89.1 1.3 34 20-53 1-35 (36)
4 COG5641 GAT1 GATA Zn-finger-co 99.0 2.2E-10 4.7E-15 93.8 2.6 49 17-65 158-212 (498)
5 KOG1601|consensus 98.9 5.3E-10 1.2E-14 78.2 3.1 46 17-62 199-245 (340)
6 COG5641 GAT1 GATA Zn-finger-co 94.5 0.02 4.3E-07 47.6 1.7 49 16-64 296-346 (498)
7 KOG3554|consensus 93.9 0.16 3.4E-06 42.9 5.6 37 17-53 386-425 (693)
8 PF01412 ArfGap: Putative GTPa 88.7 0.39 8.5E-06 32.0 2.3 39 14-53 10-48 (116)
9 PF08271 TF_Zn_Ribbon: TFIIB z 88.2 0.13 2.8E-06 28.8 -0.2 28 19-48 2-29 (43)
10 COG5347 GTPase-activating prot 86.7 0.39 8.4E-06 37.9 1.6 40 12-52 15-54 (319)
11 smart00105 ArfGap Putative GTP 85.8 0.72 1.6E-05 30.6 2.3 38 16-54 2-39 (112)
12 PRK03988 translation initiatio 82.2 0.35 7.6E-06 33.9 -0.4 29 18-46 103-131 (138)
13 TIGR00311 aIF-2beta translatio 81.6 0.39 8.5E-06 33.5 -0.3 29 18-46 98-126 (133)
14 smart00653 eIF2B_5 domain pres 81.6 0.39 8.4E-06 32.4 -0.3 29 18-46 81-109 (110)
15 KOG3740|consensus 81.5 0.59 1.3E-05 40.3 0.6 31 16-46 461-495 (706)
16 PF11781 RRN7: RNA polymerase 79.5 0.64 1.4E-05 25.6 0.2 25 18-46 9-33 (36)
17 PF06677 Auto_anti-p27: Sjogre 77.6 0.92 2E-05 25.8 0.4 26 16-45 16-41 (41)
18 PRK12336 translation initiatio 76.6 0.67 1.4E-05 34.0 -0.4 29 18-46 99-127 (201)
19 PF15396 FAM60A: Protein Famil 75.9 1.9 4E-05 32.6 1.8 15 37-52 49-63 (213)
20 PF14803 Nudix_N_2: Nudix N-te 73.9 0.91 2E-05 24.8 -0.2 28 19-46 2-30 (34)
21 PF01873 eIF-5_eIF-2B: Domain 73.4 1 2.2E-05 31.0 -0.2 29 18-46 94-122 (125)
22 PRK00423 tfb transcription ini 72.9 1.6 3.6E-05 33.6 0.9 32 15-48 9-40 (310)
23 PF06689 zf-C4_ClpX: ClpX C4-t 71.2 1.5 3.2E-05 24.6 0.2 30 18-47 2-33 (41)
24 PLN03114 ADP-ribosylation fact 70.2 3.2 6.8E-05 33.9 1.9 39 14-53 19-57 (395)
25 PRK12286 rpmF 50S ribosomal pr 68.9 1.6 3.6E-05 26.3 0.1 26 15-48 25-50 (57)
26 PRK14892 putative transcriptio 68.6 1.9 4.2E-05 28.8 0.4 36 14-50 18-54 (99)
27 KOG0706|consensus 68.4 2.8 6E-05 34.8 1.3 41 13-54 19-59 (454)
28 PRK00420 hypothetical protein; 66.2 3 6.4E-05 28.5 0.9 29 16-48 22-50 (112)
29 COG3529 Predicted nucleic-acid 65.6 1.6 3.5E-05 27.3 -0.4 34 16-49 9-43 (66)
30 KOG0703|consensus 65.5 2.3 4.9E-05 33.4 0.3 34 16-50 24-57 (287)
31 PF09526 DUF2387: Probable met 65.0 2.1 4.6E-05 26.9 -0.0 34 16-49 7-41 (71)
32 COG1405 SUA7 Transcription ini 64.6 2.7 5.8E-05 32.6 0.5 29 18-48 2-30 (285)
33 COG1645 Uncharacterized Zn-fin 64.0 2.6 5.5E-05 29.7 0.3 27 15-46 26-52 (131)
34 PF13248 zf-ribbon_3: zinc-rib 63.1 4.9 0.00011 20.2 1.2 22 18-46 3-24 (26)
35 PF01096 TFIIS_C: Transcriptio 60.1 1.2 2.6E-05 24.7 -1.6 30 19-48 2-38 (39)
36 PF07282 OrfB_Zn_ribbon: Putat 59.1 4.4 9.6E-05 24.1 0.7 34 11-47 22-55 (69)
37 PF13240 zinc_ribbon_2: zinc-r 58.4 6 0.00013 19.6 1.0 20 20-46 2-21 (23)
38 PF02701 zf-Dof: Dof domain, z 57.0 25 0.00055 21.9 3.8 45 15-59 3-51 (63)
39 TIGR02443 conserved hypothetic 57.0 3.7 8E-05 25.3 0.1 33 16-48 8-41 (59)
40 KOG1598|consensus 55.2 6.7 0.00015 33.1 1.3 28 18-47 1-28 (521)
41 smart00778 Prim_Zn_Ribbon Zinc 54.0 7.9 0.00017 21.5 1.1 28 18-45 4-32 (37)
42 cd07172 NR_DBD_GR_PR DNA-bindi 53.4 10 0.00022 23.8 1.7 32 18-53 3-34 (78)
43 cd07168 NR_DBD_DHR4_like DNA-b 53.3 9.8 0.00021 24.5 1.6 34 16-53 5-38 (90)
44 cd07171 NR_DBD_ER DNA-binding 53.2 11 0.00023 23.9 1.8 32 18-53 4-35 (82)
45 smart00659 RPOLCX RNA polymera 52.4 5.6 0.00012 22.7 0.3 24 19-46 4-27 (44)
46 cd07170 NR_DBD_ERR DNA-binding 51.3 11 0.00024 24.7 1.7 31 18-52 5-35 (97)
47 cd07169 NR_DBD_GCNF_like DNA-b 51.0 13 0.00027 24.0 1.9 33 16-52 5-37 (90)
48 PF01783 Ribosomal_L32p: Ribos 50.9 4.1 8.9E-05 24.1 -0.4 24 16-47 25-48 (56)
49 smart00440 ZnF_C2C2 C2C2 Zinc 50.9 3.8 8.3E-05 22.7 -0.5 30 19-48 2-38 (40)
50 TIGR01384 TFS_arch transcripti 50.5 5.2 0.00011 25.7 -0.0 35 15-49 60-101 (104)
51 PF12760 Zn_Tnp_IS1595: Transp 50.0 6.8 0.00015 22.0 0.4 27 17-45 18-44 (46)
52 TIGR01385 TFSII transcription 49.9 6.4 0.00014 30.7 0.4 38 13-50 254-298 (299)
53 cd07160 NR_DBD_LXR DNA-binding 49.8 11 0.00024 24.9 1.5 34 16-53 17-50 (101)
54 cd07173 NR_DBD_AR DNA-binding 48.9 14 0.00029 23.5 1.8 31 18-52 4-34 (82)
55 PLN03119 putative ADP-ribosyla 47.0 10 0.00022 32.8 1.1 34 14-48 20-53 (648)
56 cd07155 NR_DBD_ER_like DNA-bin 46.9 12 0.00026 23.1 1.3 29 20-52 1-29 (75)
57 cd07165 NR_DBD_DmE78_like DNA- 46.7 14 0.0003 23.2 1.5 29 20-52 1-29 (81)
58 cd06968 NR_DBD_ROR DNA-binding 45.8 15 0.00032 24.0 1.6 32 17-52 5-36 (95)
59 PF09297 zf-NADH-PPase: NADH p 45.6 4.6 0.0001 21.1 -0.7 27 17-47 3-30 (32)
60 KOG1597|consensus 45.6 10 0.00022 30.2 0.9 33 19-51 2-34 (308)
61 cd06955 NR_DBD_VDR DNA-binding 45.5 8.8 0.00019 25.7 0.5 33 16-52 5-37 (107)
62 cd07166 NR_DBD_REV_ERB DNA-bin 45.2 8.9 0.00019 24.6 0.5 32 17-52 3-34 (89)
63 cd07162 NR_DBD_PXR DNA-binding 45.1 15 0.00033 23.3 1.6 29 20-52 2-30 (87)
64 PF12773 DZR: Double zinc ribb 45.1 15 0.00033 20.4 1.4 27 16-46 11-37 (50)
65 PHA00626 hypothetical protein 45.1 7.4 0.00016 24.0 0.1 32 19-50 2-35 (59)
66 PLN03131 hypothetical protein; 45.0 11 0.00024 32.8 1.2 35 14-49 20-54 (705)
67 PF04161 Arv1: Arv1-like famil 44.8 10 0.00022 27.7 0.8 27 19-45 2-31 (208)
68 PRK00085 recO DNA repair prote 44.7 11 0.00024 27.2 1.0 29 17-45 149-177 (247)
69 COG1326 Uncharacterized archae 44.4 4.3 9.4E-05 30.4 -1.2 35 14-48 3-40 (201)
70 cd07158 NR_DBD_Ppar_like The D 44.4 15 0.00032 22.5 1.3 29 20-52 1-29 (73)
71 cd07161 NR_DBD_EcR DNA-binding 44.1 16 0.00036 23.6 1.6 31 19-53 3-33 (91)
72 KOG0818|consensus 43.9 15 0.00033 31.6 1.7 37 15-52 6-42 (669)
73 cd06963 NR_DBD_GR_like The DNA 43.9 14 0.00031 22.8 1.2 30 20-53 1-30 (73)
74 COG1066 Sms Predicted ATP-depe 43.8 9.3 0.0002 31.8 0.5 25 16-47 6-30 (456)
75 cd06956 NR_DBD_RXR DNA-binding 43.5 16 0.00035 22.7 1.4 31 19-53 2-32 (77)
76 cd07179 2DBD_NR_DBD2 The secon 43.5 16 0.00035 22.5 1.4 30 20-53 1-30 (74)
77 KOG0909|consensus 42.7 6.4 0.00014 33.0 -0.6 45 16-60 160-216 (500)
78 cd06966 NR_DBD_CAR DNA-binding 41.5 9.7 0.00021 24.8 0.2 30 19-52 2-31 (94)
79 cd06964 NR_DBD_RAR DNA-binding 41.3 7.5 0.00016 24.8 -0.3 33 16-52 3-35 (85)
80 cd06965 NR_DBD_Ppar DNA-bindin 40.6 12 0.00025 23.8 0.5 29 20-52 2-30 (84)
81 COG2816 NPY1 NTP pyrophosphohy 39.5 11 0.00024 29.4 0.3 32 15-49 109-140 (279)
82 PF00105 zf-C4: Zinc finger, C 39.0 12 0.00026 22.4 0.3 29 19-51 2-30 (70)
83 cd06961 NR_DBD_TR DNA-binding 38.7 17 0.00038 23.0 1.1 30 20-53 2-31 (85)
84 TIGR01031 rpmF_bact ribosomal 38.3 12 0.00026 22.2 0.3 26 15-48 24-49 (55)
85 cd07164 NR_DBD_PNR_like_1 DNA- 37.8 19 0.00041 22.4 1.1 30 20-53 1-30 (78)
86 KOG0704|consensus 37.6 8.1 0.00017 31.5 -0.7 39 14-53 16-54 (386)
87 cd07163 NR_DBD_TLX DNA-binding 37.2 9.3 0.0002 24.7 -0.4 33 16-52 5-37 (92)
88 PF09723 Zn-ribbon_8: Zinc rib 36.8 11 0.00024 20.9 -0.0 28 19-46 7-34 (42)
89 cd06960 NR_DBD_HNF4A DNA-bindi 36.2 12 0.00025 23.1 -0.0 29 20-52 1-29 (76)
90 PF03604 DNA_RNApol_7kD: DNA d 35.3 21 0.00045 19.1 0.9 24 19-46 2-25 (32)
91 COG1601 GCD7 Translation initi 35.3 11 0.00024 26.9 -0.2 30 17-46 105-134 (151)
92 PRK01110 rpmF 50S ribosomal pr 35.2 13 0.00028 22.5 0.0 24 17-49 27-50 (60)
93 PRK11823 DNA repair protein Ra 34.2 20 0.00044 29.0 1.0 26 15-47 5-30 (446)
94 smart00399 ZnF_C4 c4 zinc fing 34.2 23 0.0005 21.3 1.1 28 20-51 2-29 (70)
95 COG3952 Predicted membrane pro 33.8 9.3 0.0002 26.3 -0.8 18 31-49 77-94 (113)
96 cd01121 Sms Sms (bacterial rad 33.2 18 0.00039 28.8 0.6 22 19-47 2-23 (372)
97 cd06959 NR_DBD_EcR_like The DN 33.1 24 0.00052 21.6 1.0 29 20-52 2-30 (73)
98 PF14471 DUF4428: Domain of un 32.9 27 0.00059 20.3 1.2 27 19-46 1-28 (51)
99 PHA02998 RNA polymerase subuni 32.8 18 0.00039 27.0 0.5 34 16-49 142-182 (195)
100 cd07157 2DBD_NR_DBD1 The first 32.6 11 0.00023 24.1 -0.7 30 19-52 2-31 (86)
101 PRK00432 30S ribosomal protein 32.2 17 0.00037 21.2 0.2 28 16-47 19-46 (50)
102 PRK08351 DNA-directed RNA poly 32.2 28 0.0006 21.4 1.2 15 18-32 16-31 (61)
103 PF02591 DUF164: Putative zinc 32.0 12 0.00027 21.7 -0.4 30 16-46 21-54 (56)
104 cd06958 NR_DBD_COUP_TF DNA-bin 31.6 22 0.00049 21.8 0.7 16 37-52 14-29 (73)
105 cd06967 NR_DBD_TR2_like DNA-bi 31.5 13 0.00029 23.7 -0.3 32 17-52 3-34 (87)
106 COG2888 Predicted Zn-ribbon RN 31.3 16 0.00035 22.6 0.0 8 39-46 51-58 (61)
107 PRK06393 rpoE DNA-directed RNA 31.1 30 0.00064 21.5 1.2 16 17-32 17-33 (64)
108 smart00834 CxxC_CXXC_SSSS Puta 30.0 18 0.00038 19.1 0.0 27 19-46 7-34 (41)
109 smart00661 RPOL9 RNA polymeras 29.8 24 0.00052 19.6 0.6 28 19-48 2-30 (52)
110 PF09698 GSu_C4xC__C2xCH: Geob 29.6 32 0.00069 18.6 1.0 18 25-44 18-35 (36)
111 PHA02942 putative transposase; 29.5 30 0.00065 27.6 1.3 33 11-47 319-351 (383)
112 COG5349 Uncharacterized protei 29.2 25 0.00054 24.6 0.7 36 15-52 19-54 (126)
113 cd06962 NR_DBD_FXR DNA-binding 29.2 15 0.00032 23.4 -0.4 31 19-53 3-33 (84)
114 PRK03564 formate dehydrogenase 29.1 22 0.00048 28.0 0.5 35 17-51 226-265 (309)
115 cd07156 NR_DBD_VDR_like The DN 29.1 26 0.00056 21.4 0.7 17 37-53 14-30 (72)
116 PF09889 DUF2116: Uncharacteri 29.0 33 0.00071 20.9 1.1 28 17-51 3-31 (59)
117 PF04810 zf-Sec23_Sec24: Sec23 29.0 27 0.00058 19.1 0.7 30 17-46 2-32 (40)
118 COG0675 Transposase and inacti 28.9 28 0.0006 25.2 0.9 26 13-46 305-330 (364)
119 KOG0317|consensus 28.6 58 0.0013 25.8 2.7 45 15-60 237-281 (293)
120 TIGR00613 reco DNA repair prot 28.0 30 0.00064 24.9 0.9 30 17-46 147-176 (241)
121 cd07167 NR_DBD_Lrh-1_like The 28.0 34 0.00073 22.2 1.1 16 37-52 14-29 (93)
122 TIGR03573 WbuX N-acetyl sugar 27.8 56 0.0012 25.4 2.5 32 17-50 1-33 (343)
123 PRK14890 putative Zn-ribbon RN 27.8 20 0.00044 22.0 0.0 8 39-46 49-56 (59)
124 TIGR00244 transcriptional regu 27.7 34 0.00075 24.4 1.2 36 18-53 1-43 (147)
125 PF08274 PhnA_Zn_Ribbon: PhnA 27.5 16 0.00034 19.4 -0.4 24 18-46 3-27 (30)
126 PRK00398 rpoP DNA-directed RNA 27.4 22 0.00047 19.8 0.1 27 18-47 4-30 (46)
127 TIGR02605 CxxC_CxxC_SSSS putat 27.2 23 0.0005 19.9 0.2 27 19-46 7-34 (52)
128 PF08273 Prim_Zn_Ribbon: Zinc- 27.2 26 0.00056 19.7 0.4 26 19-44 5-32 (40)
129 cd02337 ZZ_CBP Zinc finger, ZZ 27.1 44 0.00096 18.6 1.4 28 19-46 2-30 (41)
130 PRK06556 vitamin B12-dependent 26.7 24 0.00053 31.8 0.3 27 14-46 921-948 (953)
131 PF03811 Zn_Tnp_IS1: InsA N-te 26.7 41 0.00088 18.4 1.1 28 16-44 4-35 (36)
132 PF07754 DUF1610: Domain of un 26.4 31 0.00067 17.5 0.6 23 20-45 1-23 (24)
133 cd06916 NR_DBD_like DNA-bindin 25.6 14 0.00031 22.5 -0.9 29 20-52 1-29 (72)
134 PRK13715 conjugal transfer pro 25.4 51 0.0011 20.6 1.6 37 17-53 34-70 (73)
135 KOG2767|consensus 25.3 41 0.00089 27.6 1.4 32 18-49 97-129 (400)
136 smart00290 ZnF_UBP Ubiquitin C 25.3 28 0.00061 19.2 0.3 19 19-46 1-19 (50)
137 COG1997 RPL43A Ribosomal prote 25.0 27 0.00058 23.1 0.2 33 13-48 31-63 (89)
138 COG1734 DksA DnaK suppressor p 24.9 31 0.00068 23.6 0.5 34 18-51 81-114 (120)
139 PF13878 zf-C2H2_3: zinc-finge 24.9 15 0.00032 20.5 -0.9 13 37-49 12-24 (41)
140 TIGR00416 sms DNA repair prote 24.7 35 0.00076 27.8 0.9 26 15-47 5-30 (454)
141 KOG2691|consensus 24.3 32 0.0007 23.7 0.5 34 15-48 71-111 (113)
142 cd06970 NR_DBD_PNR DNA-binding 24.1 22 0.00048 23.0 -0.3 32 17-52 6-37 (92)
143 COG4260 Membrane protease subu 24.0 42 0.0009 27.0 1.1 27 17-46 315-342 (345)
144 PRK14559 putative protein seri 24.0 42 0.00091 29.0 1.2 36 13-48 11-51 (645)
145 PF14122 YokU: YokU-like prote 22.9 25 0.00054 23.2 -0.2 13 39-51 36-48 (87)
146 PF10058 DUF2296: Predicted in 22.4 38 0.00081 20.0 0.5 36 11-46 16-52 (54)
147 PF01258 zf-dskA_traR: Prokary 21.9 14 0.00031 19.6 -1.3 29 18-46 4-32 (36)
148 COG3058 FdhE Uncharacterized p 21.8 56 0.0012 26.0 1.5 32 18-50 226-264 (308)
149 PRK04023 DNA polymerase II lar 21.7 50 0.0011 30.5 1.3 31 16-46 637-671 (1121)
150 PF01286 XPA_N: XPA protein N- 20.5 46 0.001 18.2 0.6 26 17-44 3-30 (34)
151 PF10080 DUF2318: Predicted me 20.3 17 0.00038 24.2 -1.4 14 38-51 52-65 (102)
No 1
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.71 E-value=6.3e-18 Score=101.84 Aligned_cols=43 Identities=42% Similarity=0.853 Sum_probs=39.2
Q ss_pred ccccCCCCCCCccccCCCCC-CccchhHHHHhhhCCCCCCccCC
Q psy8831 19 SCANCSTTCTTLWRRNNNGE-PVCNACGLIMNTVDINAPEKIMP 61 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~-~lCNaCgl~~~~~~~~Rp~~~~~ 61 (88)
.|+||++++||+||++++|. .|||||||||++++..||.....
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRK 44 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCc
Confidence 59999999999999999544 99999999999999999998864
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.67 E-value=3.8e-17 Score=97.53 Aligned_cols=45 Identities=47% Similarity=0.854 Sum_probs=41.2
Q ss_pred CCcccccCCCCCCCccccCCCCC-CccchhHHHHhhhCCC-CCCccC
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGE-PVCNACGLIMNTVDIN-APEKIM 60 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~-~lCNaCgl~~~~~~~~-Rp~~~~ 60 (88)
....|+||++++||+||+++.|. .|||||||||++++.. ||..+.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~ 48 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLK 48 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCCCCccccc
Confidence 46789999999999999999998 9999999999999998 887764
No 3
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.62 E-value=1.2e-16 Score=89.09 Aligned_cols=34 Identities=50% Similarity=1.012 Sum_probs=28.4
Q ss_pred cccCCCCCCCccccCCCCCC-ccchhHHHHhhhCC
Q psy8831 20 CANCSTTCTTLWRRNNNGEP-VCNACGLIMNTVDI 53 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~-lCNaCgl~~~~~~~ 53 (88)
|++|++++||+||++++|.. |||||||||++++.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 89999999999999999995 99999999999975
No 4
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.98 E-value=2.2e-10 Score=93.82 Aligned_cols=49 Identities=37% Similarity=0.725 Sum_probs=43.7
Q ss_pred CcccccCCCCCCCccccCCC-----CCCccchhHHHHhhhCCCC-CCccCCCchh
Q psy8831 17 GVSCANCSTTCTTLWRRNNN-----GEPVCNACGLIMNTVDINA-PEKIMPPIES 65 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~-----G~~lCNaCgl~~~~~~~~R-p~~~~~~~~~ 65 (88)
..+|.||.|+.||+|||+.. |.+||||||||++.||.+| |..++....+
T Consensus 158 ~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks~~~k 212 (498)
T COG5641 158 PHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSDSIK 212 (498)
T ss_pred cchhccccccCCccccccccccccCCccccccccccccccCCcCCCccccccccc
Confidence 34999999999999999998 8899999999999999999 9988755443
No 5
>KOG1601|consensus
Probab=98.95 E-value=5.3e-10 Score=78.23 Aligned_cols=46 Identities=41% Similarity=0.793 Sum_probs=40.2
Q ss_pred CcccccCCCCCCCccccCCCC-CCccchhHHHHhhhCCCCCCccCCC
Q psy8831 17 GVSCANCSTTCTTLWRRNNNG-EPVCNACGLIMNTVDINAPEKIMPP 62 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G-~~lCNaCgl~~~~~~~~Rp~~~~~~ 62 (88)
...|++|++++||+||+++.| ..+|||||||++.++..|++.....
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~ 245 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRP 245 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCccccccccCc
Confidence 589999999999999999999 5999999999999986676665433
No 6
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=94.50 E-value=0.02 Score=47.56 Aligned_cols=49 Identities=29% Similarity=0.407 Sum_probs=38.8
Q ss_pred CCcccccCCC-CCCCccccCC-CCCCccchhHHHHhhhCCCCCCccCCCch
Q psy8831 16 SGVSCANCST-TCTTLWRRNN-NGEPVCNACGLIMNTVDINAPEKIMPPIE 64 (88)
Q Consensus 16 ~~~~C~nC~t-t~Tp~WRrg~-~G~~lCNaCgl~~~~~~~~Rp~~~~~~~~ 64 (88)
....+.+|.+ +.||.||+.. .+-++||+|+++.+.++..+|+..+...-
T Consensus 296 s~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d~n 346 (498)
T COG5641 296 SDKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPN 346 (498)
T ss_pred hhcCcccccccccCcccccccccccccccccccccCCcccccccCCCCChh
Confidence 3667888887 6789888775 44489999999999999999988754433
No 7
>KOG3554|consensus
Probab=93.87 E-value=0.16 Score=42.93 Aligned_cols=37 Identities=24% Similarity=0.539 Sum_probs=30.5
Q ss_pred CcccccCCCCCCCcccc-C-CCCC-CccchhHHHHhhhCC
Q psy8831 17 GVSCANCSTTCTTLWRR-N-NNGE-PVCNACGLIMNTVDI 53 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRr-g-~~G~-~lCNaCgl~~~~~~~ 53 (88)
.+-|.+|+|+++-.|=. | ++.+ .||-.|-+||+++|-
T Consensus 386 g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKygG 425 (693)
T KOG3554|consen 386 GRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYGG 425 (693)
T ss_pred CCcccccccccccceeccCCCCccchhhHHHHHHHHHhcC
Confidence 67899999999999843 3 4444 799999999999875
No 8
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=88.68 E-value=0.39 Score=31.99 Aligned_cols=39 Identities=26% Similarity=0.588 Sum_probs=27.5
Q ss_pred CCCCcccccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 14 KRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 14 ~~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
......|++|+.. -|.|-.-.-|-.||-.|.-..+..|.
T Consensus 10 ~~~N~~CaDCg~~-~p~w~s~~~GiflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 10 KPGNKVCADCGAP-NPTWASLNYGIFLCLECAGIHRSLGV 48 (116)
T ss_dssp STTCTB-TTT-SB-S--EEETTTTEEE-HHHHHHHHHHTT
T ss_pred CcCcCcCCCCCCC-CCCEEEeecChhhhHHHHHHHHHhcc
Confidence 3467899999944 46999999999999999888887774
No 9
>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=88.19 E-value=0.13 Score=28.81 Aligned_cols=28 Identities=36% Similarity=0.959 Sum_probs=19.9
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHHHH
Q psy8831 19 SCANCSTTCTTLWRRNNNGEPVCNACGLIM 48 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~ 48 (88)
.|.+|+.+. .++ ....|..+|..||+-.
T Consensus 2 ~Cp~Cg~~~-~~~-D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKE-IVF-DPERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSE-EEE-ETTTTEEEETTT-BBE
T ss_pred CCcCCcCCc-eEE-cCCCCeEECCCCCCEe
Confidence 699999876 343 3456778999999843
No 10
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=86.72 E-value=0.39 Score=37.92 Aligned_cols=40 Identities=23% Similarity=0.526 Sum_probs=32.6
Q ss_pred CCCCCCcccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 12 GNKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 12 ~~~~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
........|+.|++.. |.|-.-.-|..||-.|.=..|.-|
T Consensus 15 ~~~~~Nk~CaDCga~~-P~W~S~nlGvfiCi~CagvHRsLG 54 (319)
T COG5347 15 KSDSSNKKCADCGAPN-PTWASVNLGVFLCIDCAGVHRSLG 54 (319)
T ss_pred hhccccCccccCCCCC-CceEecccCeEEEeecchhhhccc
Confidence 3556788999999999 999999999999999965444433
No 11
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=85.77 E-value=0.72 Score=30.61 Aligned_cols=38 Identities=21% Similarity=0.535 Sum_probs=31.8
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHHHHhhhCCC
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDIN 54 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~~ 54 (88)
....|++|+. .-|.|-.-.-|..||-.|.-..+..|.+
T Consensus 2 ~N~~CaDC~~-~~p~w~s~~~GifvC~~CsgiHR~lg~h 39 (112)
T smart00105 2 GNKKCFDCGA-PNPTWASVNLGVFLCIECSGIHRSLGVH 39 (112)
T ss_pred CCCcccCCCC-CCCCcEEeccceeEhHHhHHHHHhcCCC
Confidence 3578999998 5599999999999999998888877654
No 12
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=82.23 E-value=0.35 Score=33.91 Aligned_cols=29 Identities=31% Similarity=0.600 Sum_probs=21.3
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
..|..|+..+|-+=+.+..=...|+|||-
T Consensus 103 VlC~~C~spdT~l~k~~r~~~l~C~ACGa 131 (138)
T PRK03988 103 VICPECGSPDTKLIKEGRIWVLKCEACGA 131 (138)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCC
Confidence 47999999999996643221245999985
No 13
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=81.62 E-value=0.39 Score=33.47 Aligned_cols=29 Identities=28% Similarity=0.606 Sum_probs=21.2
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
..|..|+..+|-+-+.+.--...|+|||-
T Consensus 98 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa 126 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVSLLKCEACGA 126 (133)
T ss_pred EECCCCCCCCcEEEEeCCeEEEecccCCC
Confidence 47999999999987643221135999985
No 14
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=81.62 E-value=0.39 Score=32.44 Aligned_cols=29 Identities=34% Similarity=0.595 Sum_probs=21.1
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
..|..|+..+|-+=+.+..=...|+|||-
T Consensus 81 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 47999999999997652211134999984
No 15
>KOG3740|consensus
Probab=81.45 E-value=0.59 Score=40.33 Aligned_cols=31 Identities=29% Similarity=0.740 Sum_probs=27.3
Q ss_pred CCcccccCCCCCCCccccCCCC----CCccchhHH
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNG----EPVCNACGL 46 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G----~~lCNaCgl 46 (88)
..-.|..|.|.-||.|+.-+.+ .++|.+|..
T Consensus 461 ~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvt 495 (706)
T KOG3740|consen 461 EPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVT 495 (706)
T ss_pred CchhhhhcccccccccccccccCcchHHHHHhhhh
Confidence 3679999999999999998888 588999954
No 16
>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=79.51 E-value=0.64 Score=25.61 Aligned_cols=25 Identities=28% Similarity=0.848 Sum_probs=20.3
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
..|..|+.. |-...+|.+.|..||-
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCce
Confidence 459999977 6667889999999985
No 17
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=77.63 E-value=0.92 Score=25.79 Aligned_cols=26 Identities=35% Similarity=0.896 Sum_probs=20.4
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhH
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACG 45 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCg 45 (88)
....|..|+ +|+.| ..+|+.+|-+|+
T Consensus 16 L~~~Cp~C~---~PL~~-~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 16 LDEHCPDCG---TPLMR-DKDGKIYCVSCG 41 (41)
T ss_pred hcCccCCCC---CeeEE-ecCCCEECCCCC
Confidence 466788894 89988 557788999884
No 18
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=76.62 E-value=0.67 Score=34.00 Aligned_cols=29 Identities=31% Similarity=0.598 Sum_probs=21.2
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
-.|..|+..+|-+-+.+..=..-|+|||-
T Consensus 99 V~C~~C~~pdT~l~k~~~~~~l~C~aCGa 127 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVLMLRCDACGA 127 (201)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCC
Confidence 57999999999996643211135999986
No 19
>PF15396 FAM60A: Protein Family FAM60A
Probab=75.88 E-value=1.9 Score=32.62 Aligned_cols=15 Identities=47% Similarity=1.024 Sum_probs=11.7
Q ss_pred CCCccchhHHHHhhhC
Q psy8831 37 GEPVCNACGLIMNTVD 52 (88)
Q Consensus 37 G~~lCNaCgl~~~~~~ 52 (88)
|+ +||||.|+.++..
T Consensus 49 Ge-ICNACVLLVKRwK 63 (213)
T PF15396_consen 49 GE-ICNACVLLVKRWK 63 (213)
T ss_pred ch-hhHHHHHHHHHHh
Confidence 44 8999999877653
No 20
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=73.87 E-value=0.91 Score=24.84 Aligned_cols=28 Identities=29% Similarity=0.666 Sum_probs=12.9
Q ss_pred ccccCCCCCCCccccCCCCC-CccchhHH
Q psy8831 19 SCANCSTTCTTLWRRNNNGE-PVCNACGL 46 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~-~lCNaCgl 46 (88)
.|.+||..-+..-=.|++-. .+|.+||.
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCC
Confidence 58899976432211233333 68999985
No 21
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=73.42 E-value=1 Score=31.03 Aligned_cols=29 Identities=31% Similarity=0.563 Sum_probs=21.7
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
..|..|+..+|-+=..+..=...|+|||-
T Consensus 94 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred EEcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 46999999999997763332245999984
No 22
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=72.87 E-value=1.6 Score=33.56 Aligned_cols=32 Identities=31% Similarity=0.792 Sum_probs=22.9
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHHHH
Q psy8831 15 RSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIM 48 (88)
Q Consensus 15 ~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~ 48 (88)
.....|.+|+. +++--.-..|+++|..||+-.
T Consensus 9 ~~~~~Cp~Cg~--~~iv~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 9 EEKLVCPECGS--DKLIYDYERGEIVCADCGLVI 40 (310)
T ss_pred ccCCcCcCCCC--CCeeEECCCCeEeecccCCcc
Confidence 44568999996 333333468899999999844
No 23
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=71.24 E-value=1.5 Score=24.56 Aligned_cols=30 Identities=23% Similarity=0.525 Sum_probs=18.3
Q ss_pred cccccCCCCCCCccc--cCCCCCCccchhHHH
Q psy8831 18 VSCANCSTTCTTLWR--RNNNGEPVCNACGLI 47 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WR--rg~~G~~lCNaCgl~ 47 (88)
..|+-||.+++..=+ .|++|..+|+.|...
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHHHH
Confidence 579999998875422 566667899999763
No 24
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=70.16 E-value=3.2 Score=33.91 Aligned_cols=39 Identities=18% Similarity=0.529 Sum_probs=31.1
Q ss_pred CCCCcccccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 14 KRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 14 ~~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
......|+.|+... |.|-.-.-|..||..|.=..|..|+
T Consensus 19 kPgNk~CaDCga~n-PtWASvn~GIFLCl~CSGVHRsLGv 57 (395)
T PLN03114 19 KSDNKICFDCNAKN-PTWASVTYGIFLCIDCSAVHRSLGV 57 (395)
T ss_pred CcCCCcCccCCCCC-CCceeeccceeehhhhhHhhccCCC
Confidence 34678999999764 9999999999999999665555544
No 25
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=68.87 E-value=1.6 Score=26.29 Aligned_cols=26 Identities=31% Similarity=0.677 Sum_probs=19.1
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHHHH
Q psy8831 15 RSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIM 48 (88)
Q Consensus 15 ~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~ 48 (88)
-....|.+||...-| +.+|..||+|.
T Consensus 25 ~~l~~C~~CG~~~~~--------H~vC~~CG~Y~ 50 (57)
T PRK12286 25 PGLVECPNCGEPKLP--------HRVCPSCGYYK 50 (57)
T ss_pred CcceECCCCCCccCC--------eEECCCCCcCC
Confidence 345679999976644 46899999764
No 26
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=68.64 E-value=1.9 Score=28.75 Aligned_cols=36 Identities=19% Similarity=0.470 Sum_probs=22.9
Q ss_pred CCCCcccccCCCCCCCc-cccCCCCCCccchhHHHHhh
Q psy8831 14 KRSGVSCANCSTTCTTL-WRRNNNGEPVCNACGLIMNT 50 (88)
Q Consensus 14 ~~~~~~C~nC~tt~Tp~-WRrg~~G~~lCNaCgl~~~~ 50 (88)
......|.+|+...-++ -.+ .-++..|-.||+|+..
T Consensus 18 lpt~f~CP~Cge~~v~v~~~k-~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 18 LPKIFECPRCGKVSISVKIKK-NIAIITCGNCGLYTEF 54 (99)
T ss_pred CCcEeECCCCCCeEeeeecCC-CcceEECCCCCCccCE
Confidence 34567899999432221 122 3445889999998754
No 27
>KOG0706|consensus
Probab=68.37 E-value=2.8 Score=34.83 Aligned_cols=41 Identities=15% Similarity=0.494 Sum_probs=32.9
Q ss_pred CCCCCcccccCCCCCCCccccCCCCCCccchhHHHHhhhCCC
Q psy8831 13 NKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDIN 54 (88)
Q Consensus 13 ~~~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~~ 54 (88)
.....+.|+.|+ ...|-|-.-..|..||-.|---.|--|++
T Consensus 19 s~~~NKvCFDCg-AknPtWaSVTYGIFLCiDCSAvHRnLGVH 59 (454)
T KOG0706|consen 19 SQSENKVCFDCG-AKNPTWASVTYGIFLCIDCSAVHRNLGVH 59 (454)
T ss_pred cCCCCceecccC-CCCCCceeecceEEEEEecchhhhccccc
Confidence 345688999999 56799999999999999997755555554
No 28
>PRK00420 hypothetical protein; Validated
Probab=66.20 E-value=3 Score=28.48 Aligned_cols=29 Identities=28% Similarity=0.622 Sum_probs=22.2
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHHHH
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLIM 48 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~ 48 (88)
....|..|+ +|+.+- .+|+.+|-.||-.+
T Consensus 22 l~~~CP~Cg---~pLf~l-k~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 22 LSKHCPVCG---LPLFEL-KDGEVVCPVHGKVY 50 (112)
T ss_pred ccCCCCCCC---Ccceec-CCCceECCCCCCee
Confidence 557899999 677763 66788999998743
No 29
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=65.62 E-value=1.6 Score=27.33 Aligned_cols=34 Identities=35% Similarity=0.710 Sum_probs=24.9
Q ss_pred CCcccccCCCCCCCc-cccCCCCCCccchhHHHHh
Q psy8831 16 SGVSCANCSTTCTTL-WRRNNNGEPVCNACGLIMN 49 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~-WRrg~~G~~lCNaCgl~~~ 49 (88)
....|-.|.+.+|-. ||.+.-....|-+||...+
T Consensus 9 AGA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~ 43 (66)
T COG3529 9 AGAVCPACQAQDTLAMWRENNVEIVECVKCGHHMR 43 (66)
T ss_pred ccCCCcccchhhHHHHHHhcCCceEehhhcchHhh
Confidence 467899999999985 5544333356999998653
No 30
>KOG0703|consensus
Probab=65.47 E-value=2.3 Score=33.39 Aligned_cols=34 Identities=26% Similarity=0.572 Sum_probs=28.0
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHHHHhh
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNT 50 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~ 50 (88)
....|+.|++. .|.|-.-.-|..+|--|.=..|.
T Consensus 24 ~N~~CADC~a~-~P~WaSwnlGvFiC~~C~giHR~ 57 (287)
T KOG0703|consen 24 DNKVCADCGAK-GPRWASWNLGVFICLRCAGIHRS 57 (287)
T ss_pred ccCcccccCCC-CCCeEEeecCeEEEeeccccccc
Confidence 48899999988 99999889999999999543333
No 31
>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=64.95 E-value=2.1 Score=26.92 Aligned_cols=34 Identities=29% Similarity=0.603 Sum_probs=26.0
Q ss_pred CCcccccCCCCCCCccccCCCCC-CccchhHHHHh
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGE-PVCNACGLIMN 49 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~-~lCNaCgl~~~ 49 (88)
..-.|-.|.+..|.+|.+..+-+ .-|-+||....
T Consensus 7 AGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 7 AGAVCPKCQAMDTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred cCccCCCCcCccEEEEEEeCCceEEEecCCCCeec
Confidence 46789999999999766555455 56999998544
No 32
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=64.60 E-value=2.7 Score=32.64 Aligned_cols=29 Identities=38% Similarity=0.954 Sum_probs=20.8
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHHHH
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGLIM 48 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~ 48 (88)
..|.+|+.+ -+=..-..|+.+|-.||+-.
T Consensus 2 ~~CpeCg~~--~~~~d~~~ge~VC~~CG~Vi 30 (285)
T COG1405 2 MSCPECGST--NIITDYERGEIVCADCGLVL 30 (285)
T ss_pred CCCCCCCCc--cceeeccCCeEEeccCCEEe
Confidence 579999988 22223346889999999843
No 33
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=63.96 E-value=2.6 Score=29.65 Aligned_cols=27 Identities=37% Similarity=0.919 Sum_probs=22.2
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 15 RSGVSCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 15 ~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
.....|.-|| +||+| .+|..+|--||.
T Consensus 26 ML~~hCp~Cg---~PLF~--KdG~v~CPvC~~ 52 (131)
T COG1645 26 MLAKHCPKCG---TPLFR--KDGEVFCPVCGY 52 (131)
T ss_pred HHHhhCcccC---Cccee--eCCeEECCCCCc
Confidence 3456788888 79999 788899999995
No 34
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=63.08 E-value=4.9 Score=20.22 Aligned_cols=22 Identities=27% Similarity=0.815 Sum_probs=15.4
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
..|.+|++.. +.+..+|-.||-
T Consensus 3 ~~Cp~Cg~~~-------~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEI-------DPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcC-------CcccccChhhCC
Confidence 5789999854 334568888874
No 35
>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=60.06 E-value=1.2 Score=24.65 Aligned_cols=30 Identities=23% Similarity=0.603 Sum_probs=18.3
Q ss_pred ccccCCCCCCCcc----ccCCCCC---CccchhHHHH
Q psy8831 19 SCANCSTTCTTLW----RRNNNGE---PVCNACGLIM 48 (88)
Q Consensus 19 ~C~nC~tt~Tp~W----Rrg~~G~---~lCNaCgl~~ 48 (88)
.|.+|+..+.-.| |.++++. +.|..||-.|
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 5888998876555 4455555 4599998654
No 36
>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=59.11 E-value=4.4 Score=24.09 Aligned_cols=34 Identities=18% Similarity=0.490 Sum_probs=23.5
Q ss_pred cCCCCCCcccccCCCCCCCccccCCCCCCccchhHHH
Q psy8831 11 TGNKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLI 47 (88)
Q Consensus 11 ~~~~~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~ 47 (88)
+...+....|..||....- +.......|..||+.
T Consensus 22 v~~~~TSq~C~~CG~~~~~---~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 22 VDEAYTSQTCPRCGHRNKK---RRSGRVFTCPNCGFE 55 (69)
T ss_pred ECCCCCccCccCccccccc---ccccceEEcCCCCCE
Confidence 4466678899999987755 112223679999974
No 37
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=58.37 E-value=6 Score=19.62 Aligned_cols=20 Identities=30% Similarity=0.944 Sum_probs=12.4
Q ss_pred cccCCCCCCCccccCCCCCCccchhHH
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
|.+||... +++..+|..||.
T Consensus 2 Cp~CG~~~-------~~~~~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEI-------EDDAKFCPNCGT 21 (23)
T ss_pred CcccCCCC-------CCcCcchhhhCC
Confidence 67777654 334457877774
No 38
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=57.02 E-value=25 Score=21.89 Aligned_cols=45 Identities=16% Similarity=0.355 Sum_probs=33.8
Q ss_pred CCCcccccCCCCCCCc--cccCCCCC--CccchhHHHHhhhCCCCCCcc
Q psy8831 15 RSGVSCANCSTTCTTL--WRRNNNGE--PVCNACGLIMNTVDINAPEKI 59 (88)
Q Consensus 15 ~~~~~C~nC~tt~Tp~--WRrg~~G~--~lCNaCgl~~~~~~~~Rp~~~ 59 (88)
.....|..|..+.|-. .-.....| ++|-+|--||..-|..|-+-+
T Consensus 3 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPv 51 (63)
T PF02701_consen 3 EQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPV 51 (63)
T ss_pred ccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCcc
Confidence 3567899999988764 44444444 789999999999999886644
No 39
>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=56.96 E-value=3.7 Score=25.29 Aligned_cols=33 Identities=33% Similarity=0.575 Sum_probs=24.6
Q ss_pred CCcccccCCCCCCCccccCCCCC-CccchhHHHH
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGE-PVCNACGLIM 48 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~-~lCNaCgl~~ 48 (88)
..-.|-.|++-.|-+|.+..+-+ ..|-+||...
T Consensus 8 AGA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 8 AGAVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 46789999999999755444334 6699999844
No 40
>KOG1598|consensus
Probab=55.15 E-value=6.7 Score=33.14 Aligned_cols=28 Identities=32% Similarity=0.773 Sum_probs=20.4
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHHH
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGLI 47 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~ 47 (88)
+.|.||+.++ +. ++-..|...|.+||..
T Consensus 1 ~~C~~C~~s~-fe-~d~a~g~~~C~~CG~v 28 (521)
T KOG1598|consen 1 MVCKNCGGSN-FE-RDEATGNLYCTACGTV 28 (521)
T ss_pred CcCCCCCCCC-cc-cccccCCceeccccce
Confidence 3699999765 22 3346778899999974
No 41
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=54.04 E-value=7.9 Score=21.49 Aligned_cols=28 Identities=25% Similarity=0.659 Sum_probs=20.4
Q ss_pred cccccCCCCCCCcccc-CCCCCCccchhH
Q psy8831 18 VSCANCSTTCTTLWRR-NNNGEPVCNACG 45 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRr-g~~G~~lCNaCg 45 (88)
.-|-.|+.+..=.|.. ...|..+|+.|+
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg 32 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCG 32 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCC
Confidence 4588999888666643 345678999996
No 42
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=53.43 E-value=10 Score=23.81 Aligned_cols=32 Identities=19% Similarity=0.446 Sum_probs=21.8
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
..|..|+...+-. --|.+.|+||..|+++.-.
T Consensus 3 ~~C~VCg~~a~g~----hyGv~sC~aC~~FFRR~v~ 34 (78)
T cd07172 3 KICLVCSDEASGC----HYGVLTCGSCKVFFKRAVE 34 (78)
T ss_pred CCCeecCCcCcce----EECceeehhhHHhHHHHee
Confidence 4588888544333 2355679999999987644
No 43
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=53.26 E-value=9.8 Score=24.50 Aligned_cols=34 Identities=24% Similarity=0.420 Sum_probs=23.6
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
....|.-|+...+-. --|...|+||..|+++.-.
T Consensus 5 ~~~~C~VCg~~~~g~----hyGv~sC~aCk~FFRR~v~ 38 (90)
T cd07168 5 SPKLCSICEDKATGL----HYGIITCEGCKGFFKRTVQ 38 (90)
T ss_pred cCCCCcccCCcCcce----EECceehhhhhHhhhhhhc
Confidence 456799998654433 2355779999999987543
No 44
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserv
Probab=53.23 E-value=11 Score=23.93 Aligned_cols=32 Identities=22% Similarity=0.384 Sum_probs=22.2
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
..|.-|+...+-. --|...|+||..|+++.-.
T Consensus 4 ~~C~VCg~~~~g~----hyGv~sC~aC~~FFRR~v~ 35 (82)
T cd07171 4 HFCAVCSDYASGY----HYGVWSCEGCKAFFKRSIQ 35 (82)
T ss_pred CCCeecCCcCcce----EECceeehhhHHhHHHHee
Confidence 4688888654433 2355679999999987643
No 45
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=52.37 E-value=5.6 Score=22.70 Aligned_cols=24 Identities=21% Similarity=0.613 Sum_probs=17.7
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 19 SCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
.|.+||...+.. ..+..-|..||-
T Consensus 4 ~C~~Cg~~~~~~----~~~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIK----SKDVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecC----CCCceECCCCCc
Confidence 699999877654 223467999985
No 46
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=51.33 E-value=11 Score=24.72 Aligned_cols=31 Identities=19% Similarity=0.468 Sum_probs=21.3
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
..|.-|+...+-. --|.+.|+||..|+++.-
T Consensus 5 ~~C~VCg~~a~g~----hyGv~sC~aCk~FFRR~v 35 (97)
T cd07170 5 RLCLVCGDIASGY----HYGVASCEACKAFFKRTI 35 (97)
T ss_pred CCCeecCCcCcce----EECceeehhhhHHHHHHh
Confidence 4588898544322 245577999999998753
No 47
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=50.99 E-value=13 Score=24.03 Aligned_cols=33 Identities=21% Similarity=0.397 Sum_probs=23.5
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
....|.-|+...+-.+ -|.+.|+||..||++.-
T Consensus 5 ~~~~C~VCg~~a~g~h----yGv~sC~aCk~FFRR~v 37 (90)
T cd07169 5 EQRTCLICGDRATGLH----YGIISCEGCKGFFKRSI 37 (90)
T ss_pred cCCCCeecCCcCcceE----ECcceehhhHHHHHHHh
Confidence 4566999986554432 35567999999998764
No 48
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=50.91 E-value=4.1 Score=24.13 Aligned_cols=24 Identities=33% Similarity=0.771 Sum_probs=16.7
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHHH
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLI 47 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~ 47 (88)
....|.+||.-.-| +.+|.+||.|
T Consensus 25 ~l~~c~~cg~~~~~--------H~vc~~cG~y 48 (56)
T PF01783_consen 25 NLVKCPNCGEPKLP--------HRVCPSCGYY 48 (56)
T ss_dssp SEEESSSSSSEEST--------TSBCTTTBBS
T ss_pred ceeeeccCCCEecc--------cEeeCCCCeE
Confidence 45679999954322 4699999954
No 49
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=50.86 E-value=3.8 Score=22.74 Aligned_cols=30 Identities=27% Similarity=0.659 Sum_probs=20.3
Q ss_pred ccccCCCCCCCcc----ccCCCCC---CccchhHHHH
Q psy8831 19 SCANCSTTCTTLW----RRNNNGE---PVCNACGLIM 48 (88)
Q Consensus 19 ~C~nC~tt~Tp~W----Rrg~~G~---~lCNaCgl~~ 48 (88)
.|.+|+-.+.-.| |..+++. +.|-.||-.|
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 5888987765554 4556665 5699998655
No 50
>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=50.47 E-value=5.2 Score=25.73 Aligned_cols=35 Identities=29% Similarity=0.758 Sum_probs=24.6
Q ss_pred CCCcccccCCCCCCCcc----ccCCCCC---CccchhHHHHh
Q psy8831 15 RSGVSCANCSTTCTTLW----RRNNNGE---PVCNACGLIMN 49 (88)
Q Consensus 15 ~~~~~C~nC~tt~Tp~W----Rrg~~G~---~lCNaCgl~~~ 49 (88)
.....|..|+-.+--.| |..++|. ++|-.||..|+
T Consensus 60 ~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 60 TTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred cccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeE
Confidence 34679999997764444 4555666 56999998775
No 51
>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=49.98 E-value=6.8 Score=22.02 Aligned_cols=27 Identities=30% Similarity=0.756 Sum_probs=17.9
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhH
Q psy8831 17 GVSCANCSTTCTTLWRRNNNGEPVCNACG 45 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G~~lCNaCg 45 (88)
..+|..|+.+ ...|-++ .+.+.|++|+
T Consensus 18 g~~CP~Cg~~-~~~~~~~-~~~~~C~~C~ 44 (46)
T PF12760_consen 18 GFVCPHCGST-KHYRLKT-RGRYRCKACR 44 (46)
T ss_pred CCCCCCCCCe-eeEEeCC-CCeEECCCCC
Confidence 3679999987 4444333 4457798885
No 52
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=49.87 E-value=6.4 Score=30.74 Aligned_cols=38 Identities=18% Similarity=0.421 Sum_probs=26.6
Q ss_pred CCCCCcccccCCCCCCCcc----ccCCCCC---CccchhHHHHhh
Q psy8831 13 NKRSGVSCANCSTTCTTLW----RRNNNGE---PVCNACGLIMNT 50 (88)
Q Consensus 13 ~~~~~~~C~nC~tt~Tp~W----Rrg~~G~---~lCNaCgl~~~~ 50 (88)
+......|..|+-.+...| |..+++- +.|..||..|++
T Consensus 254 ~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~f 298 (299)
T TIGR01385 254 AVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWKF 298 (299)
T ss_pred CCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeeee
Confidence 4445789999998887665 3344443 469999988763
No 53
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=49.78 E-value=11 Score=24.94 Aligned_cols=34 Identities=15% Similarity=0.392 Sum_probs=23.8
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
....|.-|+...+-. --|.+.|+||..||++.-.
T Consensus 17 ~~~~C~VCg~~a~g~----hyGv~sC~aCk~FFRR~v~ 50 (101)
T cd07160 17 GNEVCSVCGDKASGF----HYNVLSCEGCKGFFRRSVI 50 (101)
T ss_pred CCCCCeecCCcCcce----EECcceehhhhhhhhhccc
Confidence 356799999654433 2355789999999987643
No 54
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=48.92 E-value=14 Score=23.51 Aligned_cols=31 Identities=16% Similarity=0.547 Sum_probs=21.8
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
..|..|+...+-. --|.+.|+||..|+++.-
T Consensus 4 ~~C~VCg~~a~g~----hyGv~sC~aCk~FFRR~v 34 (82)
T cd07173 4 KTCLICGDEASGC----HYGALTCGSCKVFFKRAA 34 (82)
T ss_pred CCCeecCCcCcce----EECcchhhhHHHHHHHHh
Confidence 4588888654433 235567999999998764
No 55
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=47.04 E-value=10 Score=32.84 Aligned_cols=34 Identities=24% Similarity=0.339 Sum_probs=27.7
Q ss_pred CCCCcccccCCCCCCCccccCCCCCCccchhHHHH
Q psy8831 14 KRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIM 48 (88)
Q Consensus 14 ~~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~ 48 (88)
......|++|+... |.|-.-.-|-.+|-.|.=..
T Consensus 20 lPgNk~CADCgs~~-P~WASiNlGIFICi~CSGIH 53 (648)
T PLN03119 20 LPPNRRCINCNSLG-PQYVCTTFWTFVCMACSGIH 53 (648)
T ss_pred CcCCCccccCCCCC-CCceeeccceEEeccchhhh
Confidence 45678999999765 99999899999999995433
No 56
>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E
Probab=46.94 E-value=12 Score=23.10 Aligned_cols=29 Identities=21% Similarity=0.547 Sum_probs=18.3
Q ss_pred cccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
|.-|+...+-. --|.+.|+||..++++.-
T Consensus 1 C~VC~~~~~g~----hygv~sC~aCk~FFRR~~ 29 (75)
T cd07155 1 CLVCGDIASGY----HYGVASCEACKAFFKRTI 29 (75)
T ss_pred CcccCccCcce----EEChhhhhhhHHHHHHHh
Confidence 45566443322 235567999999998753
No 57
>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers. DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,
Probab=46.73 E-value=14 Score=23.22 Aligned_cols=29 Identities=17% Similarity=0.486 Sum_probs=18.8
Q ss_pred cccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
|.-|+...+-. --|...|+||..|+++.-
T Consensus 1 C~VCg~~~~g~----hyG~~sC~aC~~FFRR~~ 29 (81)
T cd07165 1 CKVCGDKASGY----HYGVTSCEGCKGFFRRSI 29 (81)
T ss_pred CCccCccCcce----EECchhhhhHHHHHHhHh
Confidence 45566544322 235567999999998764
No 58
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe
Probab=45.76 E-value=15 Score=23.99 Aligned_cols=32 Identities=16% Similarity=0.472 Sum_probs=22.8
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 17 GVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
...|.-|+...+-.+ -|...|+||..|+++.-
T Consensus 5 ~~~C~VCg~~~~g~h----yGv~sC~aC~~FFRR~v 36 (95)
T cd06968 5 VIPCKICGDKSSGIH----YGVITCEGCKGFFRRSQ 36 (95)
T ss_pred ccCCcccCCcCcceE----ECceeehhhHHhhHHhe
Confidence 456899986554432 35567999999998764
No 59
>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=45.63 E-value=4.6 Score=21.09 Aligned_cols=27 Identities=22% Similarity=0.511 Sum_probs=15.0
Q ss_pred CcccccCCCCCCCccccCCCCC-CccchhHHH
Q psy8831 17 GVSCANCSTTCTTLWRRNNNGE-PVCNACGLI 47 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G~-~lCNaCgl~ 47 (88)
.+.|..||+...+. +.|. .+|.+||..
T Consensus 3 ~rfC~~CG~~t~~~----~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA----PGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-----SSSS-EEESSSS-E
T ss_pred CcccCcCCccccCC----CCcCEeECCCCcCE
Confidence 46799999877665 2233 689999873
No 60
>KOG1597|consensus
Probab=45.62 E-value=10 Score=30.17 Aligned_cols=33 Identities=27% Similarity=0.801 Sum_probs=25.2
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHHHHhhh
Q psy8831 19 SCANCSTTCTTLWRRNNNGEPVCNACGLIMNTV 51 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~ 51 (88)
.|..|....-.+--+-..|.++|-.|||-+.-+
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r 34 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTVCSECGLVLEDR 34 (308)
T ss_pred CCCCCCCCCCCeeeeccCCceecccCCeeeccc
Confidence 588888776667666778889999999965433
No 61
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core
Probab=45.50 E-value=8.8 Score=25.72 Aligned_cols=33 Identities=15% Similarity=0.312 Sum_probs=23.3
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
....|..|+...+-.+ -|...|+||..|+++.-
T Consensus 5 ~~~~C~VCg~~a~g~h----yGv~sC~aCk~FFRR~v 37 (107)
T cd06955 5 VPRICGVCGDRATGFH----FNAMTCEGCKGFFRRSM 37 (107)
T ss_pred CCCCCeecCCcCcccE----ECcceeeeecceeccee
Confidence 4466999986554332 35567999999988754
No 62
>cd07166 NR_DBD_REV_ERB DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers. DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyr
Probab=45.21 E-value=8.9 Score=24.64 Aligned_cols=32 Identities=19% Similarity=0.419 Sum_probs=22.5
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 17 GVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
...|.-|+...+-.+ -|...|+||..|+++.-
T Consensus 3 ~~~C~VCg~~a~g~h----yGv~sC~aCk~FFRR~v 34 (89)
T cd07166 3 VVLCKVCGDKASGFH----YGVHACEGCKGFFRRSI 34 (89)
T ss_pred CCCCcccCccCcceE----EChhhhhhHhhEeccee
Confidence 346889986554432 45567999999988753
No 63
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=45.15 E-value=15 Score=23.35 Aligned_cols=29 Identities=17% Similarity=0.427 Sum_probs=19.4
Q ss_pred cccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
|.-|+...+-. --|.+.|+||..|+++.-
T Consensus 2 C~VCg~~~~g~----hygv~sC~aC~~FFRR~v 30 (87)
T cd07162 2 CRVCGDRATGY----HFNAMTCEGCKGFFRRAM 30 (87)
T ss_pred CcccCCcCcce----EECcceehhhHHHHHhhh
Confidence 66777543332 234567999999998764
No 64
>PF12773 DZR: Double zinc ribbon
Probab=45.13 E-value=15 Score=20.40 Aligned_cols=27 Identities=22% Similarity=0.679 Sum_probs=15.0
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
....|.+||+... .......+|..||-
T Consensus 11 ~~~fC~~CG~~l~----~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 11 DAKFCPHCGTPLP----PPDQSKKICPNCGA 37 (50)
T ss_pred cccCChhhcCChh----hccCCCCCCcCCcC
Confidence 4667777776665 11111245777765
No 65
>PHA00626 hypothetical protein
Probab=45.06 E-value=7.4 Score=23.95 Aligned_cols=32 Identities=25% Similarity=0.482 Sum_probs=20.6
Q ss_pred ccccCCCCCCCc--cccCCCCCCccchhHHHHhh
Q psy8831 19 SCANCSTTCTTL--WRRNNNGEPVCNACGLIMNT 50 (88)
Q Consensus 19 ~C~nC~tt~Tp~--WRrg~~G~~lCNaCgl~~~~ 50 (88)
.|-+|+..+=.. -=+++...++|..||.++.+
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeech
Confidence 588999753211 00244567999999987654
No 66
>PLN03131 hypothetical protein; Provisional
Probab=45.00 E-value=11 Score=32.82 Aligned_cols=35 Identities=20% Similarity=0.347 Sum_probs=27.9
Q ss_pred CCCCcccccCCCCCCCccccCCCCCCccchhHHHHh
Q psy8831 14 KRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMN 49 (88)
Q Consensus 14 ~~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~ 49 (88)
.-....|++|+.. -|.|-.-.-|-.||-.|.=..|
T Consensus 20 ~PgNk~CADCga~-~P~WASiNlGIFICi~CSGIHR 54 (705)
T PLN03131 20 LPPNRRCINCNSL-GPQFVCTNFWTFICMTCSGIHR 54 (705)
T ss_pred CcCCCccccCCCC-CCCeeEeccceEEchhchhhhc
Confidence 4567899999975 5999998899999999954333
No 67
>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=44.84 E-value=10 Score=27.67 Aligned_cols=27 Identities=30% Similarity=0.867 Sum_probs=22.2
Q ss_pred ccccCCCCCCCccccCCCCC---CccchhH
Q psy8831 19 SCANCSTTCTTLWRRNNNGE---PVCNACG 45 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~---~lCNaCg 45 (88)
.|.+||.....+++.-.+|. ..|..|+
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~ 31 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCG 31 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccC
Confidence 69999999988998866665 4599996
No 68
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=44.73 E-value=11 Score=27.20 Aligned_cols=29 Identities=28% Similarity=0.619 Sum_probs=23.7
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhH
Q psy8831 17 GVSCANCSTTCTTLWRRNNNGEPVCNACG 45 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G~~lCNaCg 45 (88)
...|..||......|-.-.+|..+|..|+
T Consensus 149 l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 149 LDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhhHhcCCCCCCceEEecccCCccccccc
Confidence 34799999887766777778889999996
No 69
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=44.39 E-value=4.3 Score=30.43 Aligned_cols=35 Identities=14% Similarity=0.488 Sum_probs=22.4
Q ss_pred CCCCcccccCCCCCCC--cccc-CCCCCCccchhHHHH
Q psy8831 14 KRSGVSCANCSTTCTT--LWRR-NNNGEPVCNACGLIM 48 (88)
Q Consensus 14 ~~~~~~C~nC~tt~Tp--~WRr-g~~G~~lCNaCgl~~ 48 (88)
..+-..|-+|+.-+++ +-+. |.+--.-|++||..+
T Consensus 3 ~~iy~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 3 EEIYIECPSCGSEEVSHEVIKERGREPLVRCEECGTVH 40 (201)
T ss_pred ceEEEECCCCCcchhhHHHHHhcCCceEEEccCCCcEe
Confidence 3456789999955553 3343 333123499999976
No 70
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=44.35 E-value=15 Score=22.52 Aligned_cols=29 Identities=17% Similarity=0.507 Sum_probs=18.5
Q ss_pred cccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
|.-|+...+-. --|...|+||..++++.-
T Consensus 1 C~VCg~~~~g~----hyGv~~C~aC~~FFRR~v 29 (73)
T cd07158 1 CKVCGDKASGF----HYGVHSCEGCKGFFRRTI 29 (73)
T ss_pred CcccCccCcce----EECcchhhHHHHHHhhhh
Confidence 45566444332 235567999999998754
No 71
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=44.11 E-value=16 Score=23.57 Aligned_cols=31 Identities=13% Similarity=0.363 Sum_probs=21.1
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 19 SCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
.|.-|+...+-. --|...|+||..|+++.-.
T Consensus 3 ~C~VCg~~a~g~----hyGv~sC~aCk~FFRR~v~ 33 (91)
T cd07161 3 LCLVCGDRASGY----HYNALTCEGCKGFFRRSVT 33 (91)
T ss_pred CCeeCCCcCcce----EECceeehhhHHHHHHHhc
Confidence 488888544332 2355679999999987643
No 72
>KOG0818|consensus
Probab=43.93 E-value=15 Score=31.58 Aligned_cols=37 Identities=27% Similarity=0.637 Sum_probs=29.3
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 15 RSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 15 ~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
-...+|..|+.. -|-|..-.-|-.||..|.-+.+--|
T Consensus 6 l~~evC~DC~~~-dp~WASvnrGt~lC~eCcsvHrsLG 42 (669)
T KOG0818|consen 6 LSSEVCADCSGP-DPSWASVNRGTFLCDECCSVHRSLG 42 (669)
T ss_pred hhhhhhcccCCC-CCcceeecCceEehHhhhHHHhhhc
Confidence 356789999965 5999999999999999976655443
No 73
>cd06963 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and sha
Probab=43.86 E-value=14 Score=22.77 Aligned_cols=30 Identities=17% Similarity=0.516 Sum_probs=18.6
Q ss_pred cccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
|.-|+...+-. --|...|+||..++++.-.
T Consensus 1 C~VCg~~a~~~----hygv~sC~aCk~FFRR~~~ 30 (73)
T cd06963 1 CLICGDEASGC----HYGVLTCGSCKVFFKRAAE 30 (73)
T ss_pred CcccCccCcce----EECceeehhhhHhHHHhhc
Confidence 44565433322 2345679999999987643
No 74
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=43.76 E-value=9.3 Score=31.84 Aligned_cols=25 Identities=32% Similarity=0.942 Sum_probs=19.1
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHHH
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLI 47 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~ 47 (88)
..-.|.+|| .++|.|- |+ |.+||-|
T Consensus 6 t~f~C~~CG-~~s~KW~----Gk--Cp~Cg~W 30 (456)
T COG1066 6 TAFVCQECG-YVSPKWL----GK--CPACGAW 30 (456)
T ss_pred cEEEcccCC-CCCcccc----cc--CCCCCCc
Confidence 567899999 5678883 44 9999864
No 75
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=43.52 E-value=16 Score=22.70 Aligned_cols=31 Identities=19% Similarity=0.399 Sum_probs=20.6
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 19 SCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
.|.-|+...+-. --|.+.|+||..++++.-.
T Consensus 2 ~C~VC~~~~~g~----hygv~sC~aC~~FFRR~v~ 32 (77)
T cd06956 2 ICAICGDRASGK----HYGVYSCEGCKGFFKRTVR 32 (77)
T ss_pred CCcccCCcCcce----EECceeehhHHHHHHHHhh
Confidence 367777544433 2355679999999987643
No 76
>cd07179 2DBD_NR_DBD2 The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers. The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=43.50 E-value=16 Score=22.54 Aligned_cols=30 Identities=17% Similarity=0.574 Sum_probs=18.9
Q ss_pred cccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
|.-|+...+-. --|...|+||..++++.-.
T Consensus 1 C~VCg~~~~g~----hygv~sC~aC~~FFRR~~~ 30 (74)
T cd07179 1 CRVCGGKSSGF----HFGALTCEGCKGFFRRTEL 30 (74)
T ss_pred CcccCccCcce----EECceeehhHHHHHHHHhh
Confidence 45566443332 1355679999999987643
No 77
>KOG0909|consensus
Probab=42.69 E-value=6.4 Score=32.98 Aligned_cols=45 Identities=27% Similarity=0.510 Sum_probs=31.1
Q ss_pred CCcccccCCCCC-CCccccCCC------CC-----CccchhHHHHhhhCCCCCCccC
Q psy8831 16 SGVSCANCSTTC-TTLWRRNNN------GE-----PVCNACGLIMNTVDINAPEKIM 60 (88)
Q Consensus 16 ~~~~C~nC~tt~-Tp~WRrg~~------G~-----~lCNaCgl~~~~~~~~Rp~~~~ 60 (88)
..+-|..||... +++=.-.|. |. +.||.||.-.++-..+.|..+.
T Consensus 160 N~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~RFPRYNdp~kLL 216 (500)
T KOG0909|consen 160 NNPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETRFPRYNDPIKLL 216 (500)
T ss_pred CCCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCcccCcccCCHHHHH
Confidence 457899999877 444331121 22 5799999988888888887764
No 78
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=41.47 E-value=9.7 Score=24.76 Aligned_cols=30 Identities=17% Similarity=0.440 Sum_probs=20.4
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 19 SCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
.|.-|+...+-. --|.+.|+||..||++.-
T Consensus 2 ~C~VCg~~a~g~----hyGv~sC~aC~~FFRR~v 31 (94)
T cd06966 2 ICGVCGDKALGY----NFNAITCESCKAFFRRNA 31 (94)
T ss_pred CCeeCCCcCcce----EECcceeeeehheehhcc
Confidence 477888644333 235567999999988754
No 79
>cd06964 NR_DBD_RAR DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter reg
Probab=41.29 E-value=7.5 Score=24.80 Aligned_cols=33 Identities=15% Similarity=0.325 Sum_probs=22.9
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
+...|.-|+...+-.+ -|.+.|+||..|+++.-
T Consensus 3 ~~~~C~VCg~~~~g~h----yGv~sC~aC~~FFRR~v 35 (85)
T cd06964 3 IYKPCFVCQDKSSGYH----YGVSACEGCKGFFRRSI 35 (85)
T ss_pred cCCCCcccCCcCcccE----ECcceeeeeeeEEeeee
Confidence 4457888986544332 35567999999988753
No 80
>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene
Probab=40.63 E-value=12 Score=23.79 Aligned_cols=29 Identities=17% Similarity=0.494 Sum_probs=19.5
Q ss_pred cccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
|.-|+...+-.+ -|...|+||..|+++.-
T Consensus 2 C~VCg~~~~g~h----yGv~sC~aCk~FFRR~v 30 (84)
T cd06965 2 CRVCGDKASGFH----YGVHACEGCKGFFRRTI 30 (84)
T ss_pred CcccCccCcceE----EChhhhhhhhhheeeee
Confidence 667775443332 35567999999998754
No 81
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=39.47 E-value=11 Score=29.45 Aligned_cols=32 Identities=28% Similarity=0.444 Sum_probs=22.7
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHHHHh
Q psy8831 15 RSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMN 49 (88)
Q Consensus 15 ~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~ 49 (88)
...+.|..||+...+. ...-..+|+.||.++.
T Consensus 109 ~~~RFCg~CG~~~~~~---~~g~~~~C~~cg~~~f 140 (279)
T COG2816 109 RSHRFCGRCGTKTYPR---EGGWARVCPKCGHEHF 140 (279)
T ss_pred hhCcCCCCCCCcCccc---cCceeeeCCCCCCccC
Confidence 3467899999888775 1111378999998654
No 82
>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. 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 two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....
Probab=38.97 E-value=12 Score=22.42 Aligned_cols=29 Identities=24% Similarity=0.651 Sum_probs=19.3
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHHHHhhh
Q psy8831 19 SCANCSTTCTTLWRRNNNGEPVCNACGLIMNTV 51 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~ 51 (88)
.|.-|+-. +... ..|...|++|-.|+++.
T Consensus 2 ~C~VCg~~-~~~~---~ygv~sC~~C~~FFrR~ 30 (70)
T PF00105_consen 2 KCKVCGDP-ASGY---HYGVLSCNACKMFFRRS 30 (70)
T ss_dssp BSTTTSSB-ESEE---ETTEEEEHHHHHHHHHH
T ss_pred CCeECCCc-cCcc---cccccccccceeeeeec
Confidence 57778742 2222 24567899999988874
No 83
>cd06961 NR_DBD_TR DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the he
Probab=38.73 E-value=17 Score=23.03 Aligned_cols=30 Identities=17% Similarity=0.371 Sum_probs=19.5
Q ss_pred cccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
|.-|+...+-. --|...|+||..|+++.-.
T Consensus 2 C~VCg~~~~g~----hygv~sC~aC~~FFRR~v~ 31 (85)
T cd06961 2 CVVCGDKATGY----HYRCITCEGCKGFFRRTVQ 31 (85)
T ss_pred CceeCCcCcce----EEChhhhhhhhHhhHhhhc
Confidence 66677543332 2345679999999987543
No 84
>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=38.29 E-value=12 Score=22.25 Aligned_cols=26 Identities=31% Similarity=0.646 Sum_probs=17.7
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHHHH
Q psy8831 15 RSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIM 48 (88)
Q Consensus 15 ~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~ 48 (88)
-....|.+||...-| +.+|-.||.|-
T Consensus 24 p~l~~C~~cG~~~~~--------H~vc~~cG~Y~ 49 (55)
T TIGR01031 24 PTLVVCPNCGEFKLP--------HRVCPSCGYYK 49 (55)
T ss_pred CcceECCCCCCcccC--------eeECCccCeEC
Confidence 345679999865432 36899999654
No 85
>cd07164 NR_DBD_PNR_like_1 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-t
Probab=37.84 E-value=19 Score=22.39 Aligned_cols=30 Identities=20% Similarity=0.519 Sum_probs=18.7
Q ss_pred cccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
|.-|+...+-. --|...|+||..++++.-.
T Consensus 1 C~VCg~~~~g~----hyG~~~C~~C~~FFRR~~~ 30 (78)
T cd07164 1 CRVCGDRASGK----HYGVPSCDGCRGFFKRSIR 30 (78)
T ss_pred CcccCccCcce----EECcchhhhhhhhhhhhcc
Confidence 45566433332 2355679999999987643
No 86
>KOG0704|consensus
Probab=37.60 E-value=8.1 Score=31.50 Aligned_cols=39 Identities=15% Similarity=0.411 Sum_probs=29.8
Q ss_pred CCCCcccccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 14 KRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 14 ~~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
......|+.|++ .-|+|-.-..|..+|-.|.=..|--|+
T Consensus 16 ~deNk~CfeC~a-~NPQWvSvsyGIfICLECSG~HRgLGV 54 (386)
T KOG0704|consen 16 QDENKKCFECGA-PNPQWVSVSYGIFICLECSGKHRGLGV 54 (386)
T ss_pred cccCCceeecCC-CCCCeEeecccEEEEEecCCcccccce
Confidence 347889999995 569999999999999999543443333
No 87
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=37.15 E-value=9.3 Score=24.70 Aligned_cols=33 Identities=15% Similarity=0.418 Sum_probs=22.8
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
+...|.-|+...+-. --|...|+||..|+++.-
T Consensus 5 ~~~~C~VCg~~a~g~----hyGv~sC~aCk~FFRR~v 37 (92)
T cd07163 5 LDIPCKVCGDRSSGK----HYGIYACDGCSGFFKRSI 37 (92)
T ss_pred cCCCCcccCCcCccc----EECceeeeeeeeEEeeee
Confidence 466799998644433 235567999999988753
No 88
>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=36.76 E-value=11 Score=20.86 Aligned_cols=28 Identities=21% Similarity=0.573 Sum_probs=15.9
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 19 SCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
.|..|+..-+-+..-.......|-+||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 5777876554443333323356888864
No 89
>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is
Probab=36.23 E-value=12 Score=23.13 Aligned_cols=29 Identities=28% Similarity=0.518 Sum_probs=18.2
Q ss_pred cccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
|.-|+...+-. --|.+.|+||..++++.-
T Consensus 1 C~vCg~~~~~~----hygv~~C~aC~~FFrR~~ 29 (76)
T cd06960 1 CAVCGDRATGK----HYGVLSCNGCKGFFRRSV 29 (76)
T ss_pred CCccCccCccc----EECcceeeeehheeCccc
Confidence 45566443322 235567999999987653
No 90
>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=35.33 E-value=21 Score=19.14 Aligned_cols=24 Identities=21% Similarity=0.518 Sum_probs=15.0
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 19 SCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
.|..|+....-.. ...+-|..||-
T Consensus 2 ~C~~Cg~~~~~~~----~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELKP----GDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BST----SSTSSBSSSS-
T ss_pred CCCcCCCeeEcCC----CCcEECCcCCC
Confidence 5889998877321 22356999985
No 91
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=35.28 E-value=11 Score=26.86 Aligned_cols=30 Identities=30% Similarity=0.524 Sum_probs=21.8
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 17 GVSCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
-..|..|+..+|++-+.+..=...|.|||-
T Consensus 105 yv~C~~c~s~dt~l~~~~R~~~l~c~acGa 134 (151)
T COG1601 105 YVKCKECGSPDTELIKEERLLFLKCEACGA 134 (151)
T ss_pred eeEeccCCCCchhhhhhhhhHhhHHHHhCC
Confidence 357999999999997663222245999975
No 92
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=35.16 E-value=13 Score=22.52 Aligned_cols=24 Identities=8% Similarity=-0.169 Sum_probs=16.3
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHHHHh
Q psy8831 17 GVSCANCSTTCTTLWRRNNNGEPVCNACGLIMN 49 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~ 49 (88)
...|.+|+...-|- -+|. ||+|..
T Consensus 27 ~~~c~~cg~~~~pH--------~vc~-cG~Y~g 50 (60)
T PRK01110 27 LSVDKTTGEYHLPH--------HVSP-KGYYKG 50 (60)
T ss_pred eeEcCCCCceeccc--------eecC-CcccCC
Confidence 56788888765442 4788 987653
No 93
>PRK11823 DNA repair protein RadA; Provisional
Probab=34.20 E-value=20 Score=28.98 Aligned_cols=26 Identities=23% Similarity=0.779 Sum_probs=17.9
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHHH
Q psy8831 15 RSGVSCANCSTTCTTLWRRNNNGEPVCNACGLI 47 (88)
Q Consensus 15 ~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~ 47 (88)
+..-.|.+||.+ ++.|- --|.+|+-+
T Consensus 5 ~~~y~C~~Cg~~-~~~~~------g~Cp~C~~w 30 (446)
T PRK11823 5 KTAYVCQECGAE-SPKWL------GRCPECGAW 30 (446)
T ss_pred CCeEECCcCCCC-CcccC------eeCcCCCCc
Confidence 456789999954 56652 248888764
No 94
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=34.19 E-value=23 Score=21.34 Aligned_cols=28 Identities=21% Similarity=0.585 Sum_probs=18.0
Q ss_pred cccCCCCCCCccccCCCCCCccchhHHHHhhh
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTV 51 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~ 51 (88)
|..|+...+-. .-|...|+||..++++.
T Consensus 2 C~vC~~~~~~~----hygv~~C~aC~~FFRR~ 29 (70)
T smart00399 2 CCVCGDHASGF----HFGVCSCRACKAFFRRT 29 (70)
T ss_pred CeEeCCcCccc----EeCCcEechhhhhhhhh
Confidence 55666443322 23456799999999875
No 95
>COG3952 Predicted membrane protein [Function unknown]
Probab=33.85 E-value=9.3 Score=26.28 Aligned_cols=18 Identities=28% Similarity=0.442 Sum_probs=11.7
Q ss_pred cccCCCCCCccchhHHHHh
Q psy8831 31 WRRNNNGEPVCNACGLIMN 49 (88)
Q Consensus 31 WRrg~~G~~lCNaCgl~~~ 49 (88)
||.++-+ .+|++|||+-.
T Consensus 77 ~~~DpV~-Vl~~~~glF~~ 94 (113)
T COG3952 77 RRQDPVF-VLGQACGLFIY 94 (113)
T ss_pred HhcchHH-HHHHhhhHHHH
Confidence 4444432 68999999643
No 96
>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=33.19 E-value=18 Score=28.76 Aligned_cols=22 Identities=32% Similarity=0.954 Sum_probs=15.6
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHHH
Q psy8831 19 SCANCSTTCTTLWRRNNNGEPVCNACGLI 47 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~ 47 (88)
.|.+||. ++|.|- | -|.+|+-+
T Consensus 2 ~c~~cg~-~~~~~~----g--~cp~c~~w 23 (372)
T cd01121 2 VCSECGY-VSPKWL----G--KCPECGEW 23 (372)
T ss_pred CCCCCCC-CCCCcc----E--ECcCCCCc
Confidence 6999995 567662 2 48888764
No 97
>cd06959 NR_DBD_EcR_like The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domai
Probab=33.06 E-value=24 Score=21.61 Aligned_cols=29 Identities=17% Similarity=0.497 Sum_probs=18.9
Q ss_pred cccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
|.-|+...+-. --|.+.|+||..++++.-
T Consensus 2 C~vCg~~~~~~----hygv~sC~aC~~FFRR~v 30 (73)
T cd06959 2 CVVCGDKASGF----HYGVLSCEGCKGFFRRSV 30 (73)
T ss_pred CceeCCcCcce----EECceeehhhHHHHHHhh
Confidence 55666433322 235567999999998763
No 98
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=32.90 E-value=27 Score=20.34 Aligned_cols=27 Identities=22% Similarity=0.514 Sum_probs=17.7
Q ss_pred ccccCCCCCCCcc-ccCCCCCCccchhHH
Q psy8831 19 SCANCSTTCTTLW-RRNNNGEPVCNACGL 46 (88)
Q Consensus 19 ~C~nC~tt~Tp~W-Rrg~~G~~lCNaCgl 46 (88)
.|+-|+....-+= .+-.+| ++|..|.=
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~ 28 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLK 28 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHH
Confidence 3777876654443 344566 79999964
No 99
>PHA02998 RNA polymerase subunit; Provisional
Probab=32.75 E-value=18 Score=27.03 Aligned_cols=34 Identities=24% Similarity=0.505 Sum_probs=26.2
Q ss_pred CCcccccCCCCCCCcc----ccCCCCC---CccchhHHHHh
Q psy8831 16 SGVSCANCSTTCTTLW----RRNNNGE---PVCNACGLIMN 49 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~W----Rrg~~G~---~lCNaCgl~~~ 49 (88)
....|..|+-.++-.| |.++++. +.|-.||-.|+
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccC
Confidence 5678999998887766 5666666 46999998664
No 100
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=32.59 E-value=11 Score=24.14 Aligned_cols=30 Identities=23% Similarity=0.629 Sum_probs=20.1
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 19 SCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
.|.-|+...+-. --|...|+||..|+++.-
T Consensus 2 ~C~VCg~~a~g~----hyGv~sC~aCk~FFRR~~ 31 (86)
T cd07157 2 TCQVCGEPAAGF----HHGAYVCEACKKFFMRSS 31 (86)
T ss_pred CCcccCCcCccc----EECcceeeEeeeEEecce
Confidence 477787544332 235567999999988754
No 101
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=32.24 E-value=17 Score=21.17 Aligned_cols=28 Identities=18% Similarity=0.452 Sum_probs=19.6
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHHH
Q psy8831 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLI 47 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~ 47 (88)
....|..|+.. -++... +...|..||+-
T Consensus 19 ~~~fCP~Cg~~--~m~~~~--~r~~C~~Cgyt 46 (50)
T PRK00432 19 KNKFCPRCGSG--FMAEHL--DRWHCGKCGYT 46 (50)
T ss_pred ccCcCcCCCcc--hheccC--CcEECCCcCCE
Confidence 45689999974 554332 45789999973
No 102
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=32.21 E-value=28 Score=21.41 Aligned_cols=15 Identities=20% Similarity=0.583 Sum_probs=12.2
Q ss_pred cccccCCCCC-CCccc
Q psy8831 18 VSCANCSTTC-TTLWR 32 (88)
Q Consensus 18 ~~C~nC~tt~-Tp~WR 32 (88)
..|.+|+.++ |.-|.
T Consensus 16 ~~CP~Cgs~~~T~~W~ 31 (61)
T PRK08351 16 DRCPVCGSRDLSDEWF 31 (61)
T ss_pred CcCCCCcCCccccccc
Confidence 3699999988 77885
No 103
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=31.96 E-value=12 Score=21.66 Aligned_cols=30 Identities=23% Similarity=0.583 Sum_probs=21.5
Q ss_pred CCcccccCCCCCCCcc----ccCCCCCCccchhHH
Q psy8831 16 SGVSCANCSTTCTTLW----RRNNNGEPVCNACGL 46 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~W----Rrg~~G~~lCNaCgl 46 (88)
....|..|+..-+|.. +++ +.-..|..||=
T Consensus 21 ~~~~C~gC~~~l~~~~~~~i~~~-~~i~~Cp~CgR 54 (56)
T PF02591_consen 21 EGGTCSGCHMELPPQELNEIRKG-DEIVFCPNCGR 54 (56)
T ss_pred eCCccCCCCEEcCHHHHHHHHcC-CCeEECcCCCc
Confidence 3568999999999863 333 33467999973
No 104
>cd06958 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone recept
Probab=31.62 E-value=22 Score=21.76 Aligned_cols=16 Identities=19% Similarity=0.522 Sum_probs=12.8
Q ss_pred CCCccchhHHHHhhhC
Q psy8831 37 GEPVCNACGLIMNTVD 52 (88)
Q Consensus 37 G~~lCNaCgl~~~~~~ 52 (88)
|...|+||..++++.-
T Consensus 14 gv~sC~aC~~FFRR~v 29 (73)
T cd06958 14 GQFTCEGCKSFFKRSV 29 (73)
T ss_pred Chhhhhhhhhhhhhhh
Confidence 4567999999998764
No 105
>cd06967 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or
Probab=31.52 E-value=13 Score=23.71 Aligned_cols=32 Identities=16% Similarity=0.332 Sum_probs=22.1
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 17 GVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
...|.-|+...+-.+ -|...|+||..|+++.-
T Consensus 3 ~~~C~VCg~~~~g~h----yGv~sC~aC~~FFRR~v 34 (87)
T cd06967 3 VELCVVCGDKASGRH----YGAVSCEGCKGFFKRSI 34 (87)
T ss_pred CCCCeecCCcCCcCE----eCcceEeeeeeEeeeee
Confidence 346888986544432 35567999999987753
No 106
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=31.30 E-value=16 Score=22.63 Aligned_cols=8 Identities=38% Similarity=1.049 Sum_probs=4.2
Q ss_pred CccchhHH
Q psy8831 39 PVCNACGL 46 (88)
Q Consensus 39 ~lCNaCgl 46 (88)
|.|..||+
T Consensus 51 Y~Cp~CGF 58 (61)
T COG2888 51 YRCPKCGF 58 (61)
T ss_pred eECCCcCc
Confidence 45555553
No 107
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=31.08 E-value=30 Score=21.54 Aligned_cols=16 Identities=25% Similarity=0.376 Sum_probs=12.4
Q ss_pred CcccccCCCCC-CCccc
Q psy8831 17 GVSCANCSTTC-TTLWR 32 (88)
Q Consensus 17 ~~~C~nC~tt~-Tp~WR 32 (88)
...|.+|+.++ |+-|.
T Consensus 17 ~~~Cp~Cgs~~~S~~w~ 33 (64)
T PRK06393 17 EKTCPVHGDEKTTTEWF 33 (64)
T ss_pred CCcCCCCCCCcCCcCcc
Confidence 45899999988 66774
No 108
>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=30.04 E-value=18 Score=19.10 Aligned_cols=27 Identities=22% Similarity=0.676 Sum_probs=16.0
Q ss_pred ccccCCCCCCCccccCCCCC-CccchhHH
Q psy8831 19 SCANCSTTCTTLWRRNNNGE-PVCNACGL 46 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~-~lCNaCgl 46 (88)
.|..|+..-+. |....++. ..|-.||-
T Consensus 7 ~C~~Cg~~fe~-~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEV-LQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEE-EEecCCCCCCCCCCCCC
Confidence 58888875443 33322233 56888886
No 109
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=29.83 E-value=24 Score=19.57 Aligned_cols=28 Identities=21% Similarity=0.521 Sum_probs=17.2
Q ss_pred ccccCCCCCCCccccCCCC-CCccchhHHHH
Q psy8831 19 SCANCSTTCTTLWRRNNNG-EPVCNACGLIM 48 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G-~~lCNaCgl~~ 48 (88)
.|..||..-.+. .+... ..+|..||..+
T Consensus 2 FCp~Cg~~l~~~--~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNMLIPK--EGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCccccc--cCCCCCEEECCcCCCeE
Confidence 588898755443 11122 47899999643
No 110
>PF09698 GSu_C4xC__C2xCH: Geobacter CxxxxCH...CXXCH motif (GSu_C4xC__C2xCH); InterPro: IPR010176 This motif occurs from three to eight times in eight different proteins of Geobacter sulfurreducens. The final CXXCH motif matches the cytochrome c family haem-binding site signature, suggesting that the sequence may be involved in haem-binding.
Probab=29.61 E-value=32 Score=18.57 Aligned_cols=18 Identities=22% Similarity=0.693 Sum_probs=12.3
Q ss_pred CCCCCccccCCCCCCccchh
Q psy8831 25 TTCTTLWRRNNNGEPVCNAC 44 (88)
Q Consensus 25 tt~Tp~WRrg~~G~~lCNaC 44 (88)
...+|.|-.+..+. |+.|
T Consensus 18 ~~~~p~W~~~~~~~--C~~C 35 (36)
T PF09698_consen 18 SYTTPTWGSGATTA--CGSC 35 (36)
T ss_pred cccCceeCCCCCCc--cccc
Confidence 34678897665544 9888
No 111
>PHA02942 putative transposase; Provisional
Probab=29.50 E-value=30 Score=27.63 Aligned_cols=33 Identities=24% Similarity=0.512 Sum_probs=22.7
Q ss_pred cCCCCCCcccccCCCCCCCccccCCCCCCccchhHHH
Q psy8831 11 TGNKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLI 47 (88)
Q Consensus 11 ~~~~~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~ 47 (88)
+...+....|+.||.....+ ......|..||..
T Consensus 319 V~p~yTSq~Cs~CG~~~~~l----~~r~f~C~~CG~~ 351 (383)
T PHA02942 319 VNPSYSSVSCPKCGHKMVEI----AHRYFHCPSCGYE 351 (383)
T ss_pred ECCCCCCccCCCCCCccCcC----CCCEEECCCCCCE
Confidence 44666789999999866432 1123689999873
No 112
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.23 E-value=25 Score=24.65 Aligned_cols=36 Identities=31% Similarity=0.532 Sum_probs=21.1
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 15 RSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 15 ~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
.....|-+|+--. +.|.--.-.+.|.|||+-|-.+.
T Consensus 19 Gl~grCP~CGeGr--LF~gFLK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 19 GLRGRCPRCGEGR--LFRGFLKVVPACEACGLDYGFAD 54 (126)
T ss_pred HhcCCCCCCCCch--hhhhhcccCchhhhccccccCCc
Confidence 3456788887432 33322122256999999776553
No 113
>cd06962 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved
Probab=29.18 E-value=15 Score=23.41 Aligned_cols=31 Identities=13% Similarity=0.370 Sum_probs=20.7
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 19 SCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
.|.-|+...+-. --|.+.|+||..|+++.-.
T Consensus 3 ~C~VCg~~a~g~----hyGv~sC~aCk~FFRR~v~ 33 (84)
T cd06962 3 LCVVCGDKASGY----HYNALTCEGCKGFFRRSIT 33 (84)
T ss_pred CCeecCCcCcce----EECcceeecceeeeeeeec
Confidence 477887544432 2355679999999887543
No 114
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=29.12 E-value=22 Score=28.03 Aligned_cols=35 Identities=23% Similarity=0.678 Sum_probs=22.3
Q ss_pred CcccccCCCCCCCc-cccCC--CCC--CccchhHHHHhhh
Q psy8831 17 GVSCANCSTTCTTL-WRRNN--NGE--PVCNACGLIMNTV 51 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~-WRrg~--~G~--~lCNaCgl~~~~~ 51 (88)
-..|.+|+.++.-. |--.. .+. .+|..|+-|.+..
T Consensus 226 R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~ 265 (309)
T PRK03564 226 RVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKIL 265 (309)
T ss_pred CccCCCCCCCCceeeeeecCCCcceEeeecccccccceec
Confidence 46789999765432 53222 222 5799999998764
No 115
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=29.06 E-value=26 Score=21.42 Aligned_cols=17 Identities=12% Similarity=0.266 Sum_probs=13.1
Q ss_pred CCCccchhHHHHhhhCC
Q psy8831 37 GEPVCNACGLIMNTVDI 53 (88)
Q Consensus 37 G~~lCNaCgl~~~~~~~ 53 (88)
|...|+||..++++.-.
T Consensus 14 gv~sC~aC~~FFRR~v~ 30 (72)
T cd07156 14 NAMTCEGCKGFFRRSMK 30 (72)
T ss_pred Ccceehhhhhhhchhcc
Confidence 45679999999987543
No 116
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=29.01 E-value=33 Score=20.87 Aligned_cols=28 Identities=18% Similarity=0.407 Sum_probs=19.7
Q ss_pred CcccccCCCCCCCccccCCCCCCcc-chhHHHHhhh
Q psy8831 17 GVSCANCSTTCTTLWRRNNNGEPVC-NACGLIMNTV 51 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G~~lC-NaCgl~~~~~ 51 (88)
-+.|.+||...- ..+.+| ..|.--|.++
T Consensus 3 HkHC~~CG~~Ip-------~~~~fCS~~C~~~~~k~ 31 (59)
T PF09889_consen 3 HKHCPVCGKPIP-------PDESFCSPKCREEYRKR 31 (59)
T ss_pred CCcCCcCCCcCC-------cchhhhCHHHHHHHHHH
Confidence 467999996653 346789 5998766544
No 117
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=28.96 E-value=27 Score=19.13 Aligned_cols=30 Identities=27% Similarity=0.686 Sum_probs=16.3
Q ss_pred CcccccCCCCCCCccccCCCCC-CccchhHH
Q psy8831 17 GVSCANCSTTCTTLWRRNNNGE-PVCNACGL 46 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G~-~lCNaCgl 46 (88)
...|..|++---|.=.=...|. ..||-|+.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCC
Confidence 4578999988888644445555 68999986
No 118
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=28.86 E-value=28 Score=25.21 Aligned_cols=26 Identities=19% Similarity=0.512 Sum_probs=19.2
Q ss_pred CCCCCcccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 13 NKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 13 ~~~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
.......|+.||. + ..+...|..||.
T Consensus 305 ~~~tS~~C~~cg~-----~---~~r~~~C~~cg~ 330 (364)
T COG0675 305 PYYTSKTCPCCGH-----L---SGRLFKCPRCGF 330 (364)
T ss_pred CCCCcccccccCC-----c---cceeEECCCCCC
Confidence 4677899999998 1 123368999986
No 119
>KOG0317|consensus
Probab=28.62 E-value=58 Score=25.80 Aligned_cols=45 Identities=16% Similarity=0.222 Sum_probs=31.1
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHHHHhhhCCCCCCccC
Q psy8831 15 RSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDINAPEKIM 60 (88)
Q Consensus 15 ~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~~Rp~~~~ 60 (88)
.....|.=|--+..-- --.|=|+.+|+.|.+-|-.-....|+.-.
T Consensus 237 ~a~~kC~LCLe~~~~p-SaTpCGHiFCWsCI~~w~~ek~eCPlCR~ 281 (293)
T KOG0317|consen 237 EATRKCSLCLENRSNP-SATPCGHIFCWSCILEWCSEKAECPLCRE 281 (293)
T ss_pred CCCCceEEEecCCCCC-CcCcCcchHHHHHHHHHHccccCCCcccc
Confidence 4458899997654100 00234899999999999888888887653
No 120
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=28.00 E-value=30 Score=24.89 Aligned_cols=30 Identities=23% Similarity=0.544 Sum_probs=20.3
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 17 GVSCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
...|..|+..+...+=.-..|..+|..|+-
T Consensus 147 l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~ 176 (241)
T TIGR00613 147 LDKCAVCGSKEDLIYFSMTYGGALCRQCGE 176 (241)
T ss_pred cCccCCCCCcCCCceEchhcCeEEChhhCc
Confidence 357999998443344444567789999964
No 121
>cd07167 NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which is required at several stages of development. Particularly, FTZ-F1 regulated genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development; SF-1 is an essential regu
Probab=27.99 E-value=34 Score=22.25 Aligned_cols=16 Identities=19% Similarity=0.445 Sum_probs=13.0
Q ss_pred CCCccchhHHHHhhhC
Q psy8831 37 GEPVCNACGLIMNTVD 52 (88)
Q Consensus 37 G~~lCNaCgl~~~~~~ 52 (88)
|.+.|+||..|+++.-
T Consensus 14 Gv~sC~aCk~FFRRsv 29 (93)
T cd07167 14 GLLTCESCKGFFKRTV 29 (93)
T ss_pred CchhhhhHHHHHHHHe
Confidence 5567999999998764
No 122
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=27.76 E-value=56 Score=25.39 Aligned_cols=32 Identities=25% Similarity=0.473 Sum_probs=21.3
Q ss_pred CcccccCCCCCCCc-cccCCCCCCccchhHHHHhh
Q psy8831 17 GVSCANCSTTCTTL-WRRNNNGEPVCNACGLIMNT 50 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~-WRrg~~G~~lCNaCgl~~~~ 50 (88)
+..|..|.-.+|-- =.=+.+| +||+|-.+..+
T Consensus 1 ~~~C~~C~~~~t~p~i~fd~~G--vC~~C~~~~~~ 33 (343)
T TIGR03573 1 MKFCKRCVMPTTRPGITFDEDG--VCSACRNFEEK 33 (343)
T ss_pred CCcCCCCCCCCCCCCeeECCCC--CchhhhhHHhh
Confidence 35799999887542 1113344 79999987754
No 123
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=27.76 E-value=20 Score=22.01 Aligned_cols=8 Identities=38% Similarity=1.132 Sum_probs=4.1
Q ss_pred CccchhHH
Q psy8831 39 PVCNACGL 46 (88)
Q Consensus 39 ~lCNaCgl 46 (88)
|.|-.||+
T Consensus 49 Y~CP~CGF 56 (59)
T PRK14890 49 YTCPKCGF 56 (59)
T ss_pred eECCCCCC
Confidence 45555553
No 124
>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=27.67 E-value=34 Score=24.43 Aligned_cols=36 Identities=22% Similarity=0.465 Sum_probs=25.0
Q ss_pred cccccCCCCCCCcc--ccCCCCC-----CccchhHHHHhhhCC
Q psy8831 18 VSCANCSTTCTTLW--RRNNNGE-----PVCNACGLIMNTVDI 53 (88)
Q Consensus 18 ~~C~nC~tt~Tp~W--Rrg~~G~-----~lCNaCgl~~~~~~~ 53 (88)
+.|-.|+..+|-+- |-..+|. -.|.+||-+|-.+-+
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyEr 43 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFER 43 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeee
Confidence 36899999888874 3345554 349999976665544
No 125
>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=27.54 E-value=16 Score=19.42 Aligned_cols=24 Identities=38% Similarity=0.857 Sum_probs=10.7
Q ss_pred cccccCCCCCCCccccCCCCC-CccchhHH
Q psy8831 18 VSCANCSTTCTTLWRRNNNGE-PVCNACGL 46 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~-~lCNaCgl 46 (88)
+.|..|+...|= .+|. ++|..|+-
T Consensus 3 p~Cp~C~se~~y-----~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 3 PKCPLCGSEYTY-----EDGELLVCPECGH 27 (30)
T ss_dssp ---TTT-----E-----E-SSSEEETTTTE
T ss_pred CCCCCCCCccee-----ccCCEEeCCcccc
Confidence 568888877765 3344 78999974
No 126
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=27.37 E-value=22 Score=19.78 Aligned_cols=27 Identities=22% Similarity=0.466 Sum_probs=17.1
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHHH
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGLI 47 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~ 47 (88)
-.|.+||+..+-. ...+...|..||-.
T Consensus 4 y~C~~CG~~~~~~---~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 4 YKCARCGREVELD---EYGTGVRCPYCGYR 30 (46)
T ss_pred EECCCCCCEEEEC---CCCCceECCCCCCe
Confidence 4699999865442 11114679999863
No 127
>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=27.21 E-value=23 Score=19.85 Aligned_cols=27 Identities=19% Similarity=0.599 Sum_probs=17.4
Q ss_pred ccccCCCCCCCccccCCC-CCCccchhHH
Q psy8831 19 SCANCSTTCTTLWRRNNN-GEPVCNACGL 46 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~-G~~lCNaCgl 46 (88)
.|.+|+..-+ +|+...+ ....|-.||-
T Consensus 7 ~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFE-VLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeE-EEEecCCCCCCCCCCCCC
Confidence 6888986444 5664333 3366999986
No 128
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=27.17 E-value=26 Score=19.70 Aligned_cols=26 Identities=19% Similarity=0.591 Sum_probs=14.7
Q ss_pred ccccCCCCCCCc-ccc-CCCCCCccchh
Q psy8831 19 SCANCSTTCTTL-WRR-NNNGEPVCNAC 44 (88)
Q Consensus 19 ~C~nC~tt~Tp~-WRr-g~~G~~lCNaC 44 (88)
-|-.|+.+.-=. |.. ...|..+|+.|
T Consensus 5 pCP~CGG~DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp --TTTT-TTTEEEETT----S-EEETTT
T ss_pred CCCCCcCccccccCcCcccCCCEECCCC
Confidence 478888877665 753 33466899999
No 129
>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=27.13 E-value=44 Score=18.55 Aligned_cols=28 Identities=21% Similarity=0.604 Sum_probs=19.3
Q ss_pred ccccCCCCCCCccccCCCCC-CccchhHH
Q psy8831 19 SCANCSTTCTTLWRRNNNGE-PVCNACGL 46 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~-~lCNaCgl 46 (88)
.|..|....++.|+=..=.. .||.+|..
T Consensus 2 ~C~~C~~~~~~r~~C~~C~dfDLC~~C~~ 30 (41)
T cd02337 2 TCNECKHHVETRWHCTVCEDYDLCITCYN 30 (41)
T ss_pred cCCCCCCcCCCceECCCCcchhhHHHHhC
Confidence 47778776678887554333 68999865
No 130
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=26.72 E-value=24 Score=31.82 Aligned_cols=27 Identities=33% Similarity=0.739 Sum_probs=18.9
Q ss_pred CCCCcccccCCCCCCCccccCCCCC-CccchhHH
Q psy8831 14 KRSGVSCANCSTTCTTLWRRNNNGE-PVCNACGL 46 (88)
Q Consensus 14 ~~~~~~C~nC~tt~Tp~WRrg~~G~-~lCNaCgl 46 (88)
.-..+.|.+|++.- -++|. ++|..||.
T Consensus 921 ~~~~~~c~~c~~~~------~~~g~c~~c~~cg~ 948 (953)
T PRK06556 921 AADAPLCPTCGTKM------VRNGSCYVCEGCGS 948 (953)
T ss_pred cccCCcCCCccCee------eECCceEeccCCCC
Confidence 34467799998543 23466 89999985
No 131
>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=26.66 E-value=41 Score=18.40 Aligned_cols=28 Identities=25% Similarity=0.623 Sum_probs=18.0
Q ss_pred CCcccccCCCCCCCccccC--CCCC--Cccchh
Q psy8831 16 SGVSCANCSTTCTTLWRRN--NNGE--PVCNAC 44 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg--~~G~--~lCNaC 44 (88)
+...|-.|+.++ ++-|.| ++|. ++|-.|
T Consensus 4 i~v~CP~C~s~~-~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 4 IDVHCPRCQSTE-GVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred EeeeCCCCCCCC-cceeCCCCCCCCEeEecCcC
Confidence 456788888655 244544 4565 778777
No 132
>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=26.45 E-value=31 Score=17.51 Aligned_cols=23 Identities=22% Similarity=0.616 Sum_probs=12.4
Q ss_pred cccCCCCCCCccccCCCCCCccchhH
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACG 45 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCg 45 (88)
|..|+....|. ...-.+.|-.||
T Consensus 1 C~sC~~~i~~r---~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPR---EQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCc---ccCceEeCCCCC
Confidence 55666665554 112225677776
No 133
>cd06916 NR_DBD_like DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Most nuclear receptors bind as homodimers or hetero
Probab=25.61 E-value=14 Score=22.53 Aligned_cols=29 Identities=21% Similarity=0.512 Sum_probs=17.8
Q ss_pred cccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 20 C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
|.-|+...+-. --|...|+||..++++.-
T Consensus 1 C~vC~~~~~~~----hygv~sC~aC~~FFRR~~ 29 (72)
T cd06916 1 CAVCGDKASGY----HYGVLTCEGCKGFFRRSV 29 (72)
T ss_pred CCccCccCccc----EECcceeeeeeeeEeEee
Confidence 44565433322 235567999999887654
No 134
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=25.40 E-value=51 Score=20.56 Aligned_cols=37 Identities=16% Similarity=0.310 Sum_probs=27.7
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHHHHhhhCC
Q psy8831 17 GVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~~ 53 (88)
...|..||-..-..-+..-.|..+|-.|--++-+.++
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~E~~~~ 70 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAYQERQRK 70 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHHHHHHhc
Confidence 4589999988777766666788899999776554443
No 135
>KOG2767|consensus
Probab=25.33 E-value=41 Score=27.61 Aligned_cols=32 Identities=28% Similarity=0.553 Sum_probs=23.2
Q ss_pred cccccCCCCCCCccccCCCCC-CccchhHHHHh
Q psy8831 18 VSCANCSTTCTTLWRRNNNGE-PVCNACGLIMN 49 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~-~lCNaCgl~~~ 49 (88)
..|..|+-.+|-+-=....+- .-|-|||.+.-
T Consensus 97 VlC~~C~NPETel~itk~q~i~~~CkACG~r~~ 129 (400)
T KOG2767|consen 97 VLCPSCENPETELIITKKQTISLKCKACGFRSD 129 (400)
T ss_pred eeCcCCCCCceeEEecccchhhhHHHHcCCccc
Confidence 469999999999865544333 45999997543
No 136
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=25.30 E-value=28 Score=19.16 Aligned_cols=19 Identities=42% Similarity=1.176 Sum_probs=12.9
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 19 SCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 19 ~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
.|.+|++... +| +|-.|+.
T Consensus 1 ~C~~C~~~~~-l~--------~CL~C~~ 19 (50)
T smart00290 1 RCSVCGTIEN-LW--------LCLTCGQ 19 (50)
T ss_pred CcccCCCcCC-eE--------EecCCCC
Confidence 4889997663 66 6666654
No 137
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=24.95 E-value=27 Score=23.14 Aligned_cols=33 Identities=27% Similarity=0.533 Sum_probs=25.4
Q ss_pred CCCCCcccccCCCCCCCccccCCCCCCccchhHHHH
Q psy8831 13 NKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIM 48 (88)
Q Consensus 13 ~~~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~ 48 (88)
..+....|..|+.+ .-+|...|-..|.-||--|
T Consensus 31 ~~~~~~~Cp~C~~~---~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 31 QQRAKHVCPFCGRT---TVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred HHhcCCcCCCCCCc---ceeeeccCeEEcCCCCCee
Confidence 45667899999977 4567778888899998643
No 138
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=24.91 E-value=31 Score=23.63 Aligned_cols=34 Identities=12% Similarity=0.241 Sum_probs=27.0
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHHHHhhh
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTV 51 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~ 51 (88)
..|..||-..-+.-...-.+..+|..|.-.+-+.
T Consensus 81 G~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~E~~ 114 (120)
T COG1734 81 GICEECGEPIPEARLEARPTARLCIECQERAERR 114 (120)
T ss_pred cchhccCCcCCHHHHhhCcchHHHHHHHHHHHHH
Confidence 4799999988887777777888999997755443
No 139
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=24.88 E-value=15 Score=20.46 Aligned_cols=13 Identities=31% Similarity=1.083 Sum_probs=9.4
Q ss_pred CCCccchhHHHHh
Q psy8831 37 GEPVCNACGLIMN 49 (88)
Q Consensus 37 G~~lCNaCgl~~~ 49 (88)
|...|..|||.|.
T Consensus 12 ~~~~C~~CgM~Y~ 24 (41)
T PF13878_consen 12 GATTCPTCGMLYS 24 (41)
T ss_pred CCcCCCCCCCEEC
Confidence 4567999998654
No 140
>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=24.70 E-value=35 Score=27.78 Aligned_cols=26 Identities=27% Similarity=0.727 Sum_probs=17.8
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHHH
Q psy8831 15 RSGVSCANCSTTCTTLWRRNNNGEPVCNACGLI 47 (88)
Q Consensus 15 ~~~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~ 47 (88)
+..-.|.+||. +++.|- --|.+|+-+
T Consensus 5 ~~~y~C~~Cg~-~~~~~~------g~Cp~C~~w 30 (454)
T TIGR00416 5 KSKFVCQHCGA-DSPKWQ------GKCPACHAW 30 (454)
T ss_pred CCeEECCcCCC-CCcccc------EECcCCCCc
Confidence 34578999995 456662 248888764
No 141
>KOG2691|consensus
Probab=24.25 E-value=32 Score=23.66 Aligned_cols=34 Identities=26% Similarity=0.504 Sum_probs=23.5
Q ss_pred CCCcccccCCCCCCC----ccccCCCCC---CccchhHHHH
Q psy8831 15 RSGVSCANCSTTCTT----LWRRNNNGE---PVCNACGLIM 48 (88)
Q Consensus 15 ~~~~~C~nC~tt~Tp----~WRrg~~G~---~lCNaCgl~~ 48 (88)
.....|.+|+-.+-- .=||++.+- +||-.||-.|
T Consensus 71 ts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~C~h~w 111 (113)
T KOG2691|consen 71 TSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCSCGHRW 111 (113)
T ss_pred cccccCCccCCcceEEEecccccccceEEEEEEeccccccc
Confidence 367789999988743 335555544 5788898765
No 142
>cd06970 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hing
Probab=24.08 E-value=22 Score=23.04 Aligned_cols=32 Identities=25% Similarity=0.533 Sum_probs=22.1
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHHHHhhhC
Q psy8831 17 GVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVD 52 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl~~~~~~ 52 (88)
...|.-|+...+-. --|...|+||..|+++.-
T Consensus 6 ~~~C~VCg~~a~g~----hyGv~sC~aCk~FFRR~v 37 (92)
T cd06970 6 GLLCRVCGDTSSGK----HYGIYACNGCSGFFKRSV 37 (92)
T ss_pred CCCCeecCCcCccc----EECccEEeeeeeEeeeee
Confidence 44688998654433 235567999999988754
No 143
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=24.01 E-value=42 Score=27.01 Aligned_cols=27 Identities=33% Similarity=0.711 Sum_probs=20.0
Q ss_pred CcccccCCCCCCCccccCCCCC-CccchhHH
Q psy8831 17 GVSCANCSTTCTTLWRRNNNGE-PVCNACGL 46 (88)
Q Consensus 17 ~~~C~nC~tt~Tp~WRrg~~G~-~lCNaCgl 46 (88)
...|.|||...|+-. ++|. -+|-+||-
T Consensus 315 ~nfc~ncG~~~t~~~---~ng~a~fcp~cgq 342 (345)
T COG4260 315 LNFCLNCGCGTTADF---DNGKAKFCPECGQ 342 (345)
T ss_pred cccccccCcccccCC---ccchhhhChhhcC
Confidence 348999998888754 4455 58999974
No 144
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=23.95 E-value=42 Score=28.95 Aligned_cols=36 Identities=25% Similarity=0.403 Sum_probs=21.7
Q ss_pred CCCCCcccccCCCCCCCc-----cccCCCCCCccchhHHHH
Q psy8831 13 NKRSGVSCANCSTTCTTL-----WRRNNNGEPVCNACGLIM 48 (88)
Q Consensus 13 ~~~~~~~C~nC~tt~Tp~-----WRrg~~G~~lCNaCgl~~ 48 (88)
.....+.|.+||+.-+.. =...+.|..+|..||...
T Consensus 11 n~~~akFC~~CG~~l~~~~Cp~CG~~~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 11 NPNNNRFCQKCGTSLTHKPCPQCGTEVPVDEAHCPNCGAET 51 (645)
T ss_pred CCCCCccccccCCCCCCCcCCCCCCCCCcccccccccCCcc
Confidence 345567888888775321 011245667888888743
No 145
>PF14122 YokU: YokU-like protein
Probab=22.85 E-value=25 Score=23.19 Aligned_cols=13 Identities=23% Similarity=0.876 Sum_probs=9.6
Q ss_pred CccchhHHHHhhh
Q psy8831 39 PVCNACGLIMNTV 51 (88)
Q Consensus 39 ~lCNaCgl~~~~~ 51 (88)
..|+.||+-|.-.
T Consensus 36 i~C~~CgmvYq~d 48 (87)
T PF14122_consen 36 IICSNCGMVYQDD 48 (87)
T ss_pred eeecCCCcEEehh
Confidence 5799999965433
No 146
>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=22.44 E-value=38 Score=20.04 Aligned_cols=36 Identities=17% Similarity=0.344 Sum_probs=22.8
Q ss_pred cCCCCCCcccccCCCCCCCccccCCC-CCCccchhHH
Q psy8831 11 TGNKRSGVSCANCSTTCTTLWRRNNN-GEPVCNACGL 46 (88)
Q Consensus 11 ~~~~~~~~~C~nC~tt~Tp~WRrg~~-G~~lCNaCgl 46 (88)
....+...+|.+|....--.=+...+ -.+.|-.||.
T Consensus 16 ~~~~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 16 SPSNRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred cccCceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 34566788999999876544222222 2367888875
No 147
>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=21.88 E-value=14 Score=19.61 Aligned_cols=29 Identities=17% Similarity=0.379 Sum_probs=17.3
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHH
Q psy8831 18 VSCANCSTTCTTLWRRNNNGEPVCNACGL 46 (88)
Q Consensus 18 ~~C~nC~tt~Tp~WRrg~~G~~lCNaCgl 46 (88)
..|..||-..-..-...-.+..+|-.|.-
T Consensus 4 g~C~~CGe~I~~~Rl~~~p~~~~C~~C~~ 32 (36)
T PF01258_consen 4 GICEDCGEPIPEERLVAVPGATLCVECQE 32 (36)
T ss_dssp SB-TTTSSBEEHHHHHHCTTECS-HHHHH
T ss_pred CCccccCChHHHHHHHhCCCcEECHHHhC
Confidence 34888886665544444556788888854
No 148
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=21.76 E-value=56 Score=26.01 Aligned_cols=32 Identities=25% Similarity=0.728 Sum_probs=20.9
Q ss_pred cccccCCCCCCC-ccccCCCCC------CccchhHHHHhh
Q psy8831 18 VSCANCSTTCTT-LWRRNNNGE------PVCNACGLIMNT 50 (88)
Q Consensus 18 ~~C~nC~tt~Tp-~WRrg~~G~------~lCNaCgl~~~~ 50 (88)
..|+||+.+.-- .|-= .+++ -.|..|+-|.+.
T Consensus 226 ~KC~nC~~t~~l~y~sl-~s~E~A~vkAEtC~~C~sYlKi 264 (308)
T COG3058 226 VKCSNCEQSKKLHYWSL-ESSELAAVKAETCGDCNSYLKI 264 (308)
T ss_pred HHhccccccCCccceec-cchhhhHhhhhcCCcHHHHHHH
Confidence 479999988755 4542 2222 249999877663
No 149
>PRK04023 DNA polymerase II large subunit; Validated
Probab=21.71 E-value=50 Score=30.50 Aligned_cols=31 Identities=26% Similarity=0.513 Sum_probs=19.2
Q ss_pred CCcccccCCCCCCCccccC----CCCCCccchhHH
Q psy8831 16 SGVSCANCSTTCTTLWRRN----NNGEPVCNACGL 46 (88)
Q Consensus 16 ~~~~C~nC~tt~Tp~WRrg----~~G~~lCNaCgl 46 (88)
....|.+||+.+.+.|+-. ..+.+.|..||.
T Consensus 637 ~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~ 671 (1121)
T PRK04023 637 FYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGR 671 (1121)
T ss_pred CcccCCCCCCCCCcceeCccccCcCCCCcCCCCCC
Confidence 4567778887777777532 223356777864
No 150
>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=20.49 E-value=46 Score=18.16 Aligned_cols=26 Identities=31% Similarity=0.701 Sum_probs=10.9
Q ss_pred CcccccCCCCC--CCccccCCCCCCccchh
Q psy8831 17 GVSCANCSTTC--TTLWRRNNNGEPVCNAC 44 (88)
Q Consensus 17 ~~~C~nC~tt~--Tp~WRrg~~G~~lCNaC 44 (88)
...|..|+-.- +=||. .=+..+|+.|
T Consensus 3 ~~~C~eC~~~f~dSyL~~--~F~~~VCD~C 30 (34)
T PF01286_consen 3 YPKCDECGKPFMDSYLLN--NFDLPVCDKC 30 (34)
T ss_dssp -EE-TTT--EES-SSCCC--CTS-S--TTT
T ss_pred CchHhHhCCHHHHHHHHH--hCCccccccc
Confidence 35688888664 33553 2234678887
No 151
>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=20.25 E-value=17 Score=24.21 Aligned_cols=14 Identities=36% Similarity=0.824 Sum_probs=11.0
Q ss_pred CCccchhHHHHhhh
Q psy8831 38 EPVCNACGLIMNTV 51 (88)
Q Consensus 38 ~~lCNaCgl~~~~~ 51 (88)
+++|++|+..|..-
T Consensus 52 ~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 52 QLVCKNCGVRFNLP 65 (102)
T ss_pred EEEEecCCCEEehh
Confidence 48899999977644
Done!