Query psy5674
Match_columns 145
No_of_seqs 115 out of 1075
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 23:43:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5674.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5674hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0703|consensus 100.0 1.6E-46 3.4E-51 305.6 10.0 121 12-132 7-127 (287)
2 PF01412 ArfGap: Putative GTPa 100.0 3.6E-43 7.9E-48 254.1 7.7 113 19-131 2-116 (116)
3 smart00105 ArfGap Putative GTP 100.0 1.8E-41 3.8E-46 244.1 9.2 107 28-134 1-110 (112)
4 PLN03119 putative ADP-ribosyla 100.0 5.9E-38 1.3E-42 272.4 12.9 129 1-139 1-132 (648)
5 PLN03131 hypothetical protein; 100.0 1.5E-37 3.4E-42 271.6 11.5 129 1-139 1-132 (705)
6 COG5347 GTPase-activating prot 100.0 2.4E-37 5.3E-42 256.5 10.4 118 18-135 8-129 (319)
7 PLN03114 ADP-ribosylation fact 100.0 2.1E-31 4.5E-36 221.8 11.5 123 19-141 11-139 (395)
8 KOG0705|consensus 100.0 7.8E-31 1.7E-35 228.3 8.1 115 20-135 503-620 (749)
9 KOG0704|consensus 100.0 2.9E-30 6.3E-35 213.9 10.0 124 20-143 9-139 (386)
10 KOG0706|consensus 100.0 2.7E-30 5.8E-35 219.4 7.7 85 17-101 10-94 (454)
11 KOG0521|consensus 99.9 1E-26 2.2E-31 211.4 3.2 116 20-135 416-535 (785)
12 KOG0818|consensus 99.9 3.7E-24 8.1E-29 184.4 4.4 108 26-133 4-121 (669)
13 KOG1117|consensus 99.8 1.9E-21 4.1E-26 175.4 5.5 110 22-131 290-403 (1186)
14 KOG0702|consensus 99.7 1.6E-17 3.5E-22 143.1 6.6 119 11-130 6-128 (524)
15 KOG0521|consensus 95.4 0.0032 7E-08 58.6 -0.8 73 27-101 627-700 (785)
16 PRK12495 hypothetical protein; 93.8 0.11 2.4E-06 41.7 4.6 37 20-60 29-68 (226)
17 TIGR02419 C4_traR_proteo phage 91.3 0.17 3.7E-06 32.8 2.2 35 26-60 27-62 (63)
18 PRK11019 hypothetical protein; 89.8 0.18 4E-06 34.9 1.4 50 15-64 21-71 (88)
19 PF08271 TF_Zn_Ribbon: TFIIB z 88.4 0.36 7.7E-06 28.6 1.8 28 32-60 2-29 (43)
20 PF01286 XPA_N: XPA protein N- 88.3 0.17 3.6E-06 29.1 0.3 27 31-57 4-31 (34)
21 PF00643 zf-B_box: B-box zinc 87.9 0.42 9.2E-06 27.6 1.9 34 29-62 2-36 (42)
22 PRK13715 conjugal transfer pro 87.5 0.39 8.5E-06 32.0 1.8 34 29-62 33-67 (73)
23 PHA00080 DksA-like zinc finger 85.4 0.69 1.5E-05 30.7 2.1 35 27-61 28-63 (72)
24 COG1734 DksA DnaK suppressor p 84.7 0.3 6.5E-06 35.7 0.1 32 30-61 80-112 (120)
25 PF02318 FYVE_2: FYVE-type zin 84.3 5.7 0.00012 28.4 6.6 56 5-60 24-89 (118)
26 PRK00085 recO DNA repair prote 83.3 0.67 1.4E-05 36.6 1.5 32 28-59 147-179 (247)
27 TIGR00613 reco DNA repair prot 80.9 1.6 3.5E-05 34.3 2.9 33 27-59 144-177 (241)
28 smart00401 ZnF_GATA zinc finge 77.5 2 4.4E-05 26.5 2.0 37 29-65 2-40 (52)
29 PF11781 RRN7: RNA polymerase 77.5 1.8 3.9E-05 24.9 1.6 28 28-58 6-33 (36)
30 PRK10778 dksA RNA polymerase-b 77.1 1.7 3.6E-05 32.8 1.9 45 17-62 99-144 (151)
31 PF12760 Zn_Tnp_IS1595: Transp 75.7 5.7 0.00012 23.7 3.6 38 18-57 7-44 (46)
32 COG1381 RecO Recombinational D 73.8 2 4.4E-05 34.7 1.6 30 28-57 152-182 (251)
33 PF00320 GATA: GATA zinc finge 73.7 1.6 3.4E-05 25.0 0.7 32 33-64 1-34 (36)
34 TIGR02890 spore_yteA sporulati 73.0 2.4 5.3E-05 32.2 1.8 45 17-62 74-119 (159)
35 PRK11788 tetratricopeptide rep 72.9 5 0.00011 32.9 3.8 38 17-61 341-379 (389)
36 PF01258 zf-dskA_traR: Prokary 70.1 0.44 9.6E-06 27.1 -2.2 29 32-60 5-34 (36)
37 cd07171 NR_DBD_ER DNA-binding 70.1 2.3 4.9E-05 28.8 1.0 31 29-62 2-32 (82)
38 PF14803 Nudix_N_2: Nudix N-te 69.9 2.1 4.5E-05 24.4 0.6 30 31-61 1-33 (34)
39 cd07173 NR_DBD_AR DNA-binding 68.6 2.1 4.6E-05 28.9 0.6 32 28-62 1-32 (82)
40 cd06966 NR_DBD_CAR DNA-binding 66.6 3.3 7.1E-05 28.7 1.2 29 31-62 1-29 (94)
41 COG2158 Uncharacterized protei 66.1 4.6 0.0001 29.0 1.9 23 42-64 52-76 (112)
42 cd07160 NR_DBD_LXR DNA-binding 66.1 3.7 8E-05 28.9 1.4 31 29-62 17-47 (101)
43 cd07163 NR_DBD_TLX DNA-binding 65.2 4.2 9.1E-05 28.0 1.5 30 30-62 6-35 (92)
44 cd06968 NR_DBD_ROR DNA-binding 63.8 3.7 8.1E-05 28.5 1.1 31 29-62 4-34 (95)
45 KOG3507|consensus 62.7 3.8 8.2E-05 26.4 0.9 24 31-57 21-44 (62)
46 TIGR02420 dksA RNA polymerase- 62.5 6.8 0.00015 27.6 2.3 31 27-57 77-108 (110)
47 cd07170 NR_DBD_ERR DNA-binding 61.8 3.9 8.4E-05 28.6 0.9 30 30-62 4-33 (97)
48 PF10764 Gin: Inhibitor of sig 61.3 4.3 9.3E-05 24.7 0.9 26 32-58 1-26 (46)
49 PRK00423 tfb transcription ini 60.5 6.9 0.00015 32.5 2.3 33 28-61 9-41 (310)
50 PF07282 OrfB_Zn_ribbon: Putat 60.4 6.2 0.00013 25.1 1.6 28 29-58 27-54 (69)
51 cd07157 2DBD_NR_DBD1 The first 58.2 6.4 0.00014 26.8 1.5 28 32-62 2-29 (86)
52 cd06955 NR_DBD_VDR DNA-binding 58.2 7.5 0.00016 27.7 1.8 30 30-62 6-35 (107)
53 cd07161 NR_DBD_EcR DNA-binding 56.4 5.4 0.00012 27.5 0.9 29 31-62 2-30 (91)
54 cd06970 NR_DBD_PNR DNA-binding 56.3 8.1 0.00018 26.7 1.7 32 28-62 4-35 (92)
55 cd07172 NR_DBD_GR_PR DNA-bindi 55.6 5.6 0.00012 26.5 0.8 29 31-62 3-31 (78)
56 cd06962 NR_DBD_FXR DNA-binding 55.3 7 0.00015 26.5 1.3 28 32-62 3-30 (84)
57 cd07166 NR_DBD_REV_ERB DNA-bin 53.5 5.8 0.00013 27.2 0.6 30 30-62 3-32 (89)
58 cd07169 NR_DBD_GCNF_like DNA-b 53.4 6.7 0.00014 26.9 0.9 32 28-62 4-35 (90)
59 cd06965 NR_DBD_Ppar DNA-bindin 53.3 5.3 0.00012 27.0 0.4 27 33-62 2-28 (84)
60 smart00653 eIF2B_5 domain pres 53.1 26 0.00055 25.0 3.9 42 11-58 67-109 (110)
61 cd06957 NR_DBD_PNR_like_2 DNA- 52.6 8.3 0.00018 25.9 1.3 27 33-62 1-27 (82)
62 cd07162 NR_DBD_PXR DNA-binding 52.5 6.3 0.00014 26.8 0.7 28 32-62 1-28 (87)
63 cd06967 NR_DBD_TR2_like DNA-bi 52.1 9.1 0.0002 26.1 1.4 29 31-62 4-32 (87)
64 cd06960 NR_DBD_HNF4A DNA-bindi 51.4 8.9 0.00019 25.2 1.2 27 33-62 1-27 (76)
65 cd06956 NR_DBD_RXR DNA-binding 51.2 7 0.00015 25.9 0.7 28 32-62 2-29 (77)
66 PF09297 zf-NADH-PPase: NADH p 50.9 12 0.00025 20.5 1.5 30 29-60 2-31 (32)
67 cd07168 NR_DBD_DHR4_like DNA-b 50.5 9.4 0.0002 26.2 1.3 31 29-62 5-35 (90)
68 PF06827 zf-FPG_IleRS: Zinc fi 50.0 8.4 0.00018 20.7 0.8 28 31-58 2-29 (30)
69 cd06963 NR_DBD_GR_like The DNA 49.8 7.9 0.00017 25.4 0.8 27 33-62 1-27 (73)
70 cd07156 NR_DBD_VDR_like The DN 49.6 8.9 0.00019 25.0 1.0 27 33-62 1-27 (72)
71 cd06964 NR_DBD_RAR DNA-binding 49.5 11 0.00024 25.5 1.5 29 31-62 5-33 (85)
72 cd06916 NR_DBD_like DNA-bindin 49.0 10 0.00022 24.7 1.2 27 33-62 1-27 (72)
73 cd07158 NR_DBD_Ppar_like The D 48.6 6.8 0.00015 25.6 0.3 27 33-62 1-27 (73)
74 TIGR01385 TFSII transcription 48.3 52 0.0011 27.5 5.6 31 28-58 256-294 (299)
75 COG1997 RPL43A Ribosomal prote 48.1 14 0.00031 25.6 1.9 32 29-62 34-65 (89)
76 COG2174 RPL34A Ribosomal prote 47.2 12 0.00027 26.1 1.5 33 26-58 30-79 (93)
77 smart00659 RPOLCX RNA polymera 47.1 9.9 0.00021 22.8 0.8 24 32-58 4-27 (44)
78 cd03031 GRX_GRX_like Glutaredo 47.0 24 0.00053 26.3 3.2 37 18-63 87-123 (147)
79 cd06958 NR_DBD_COUP_TF DNA-bin 46.1 8.5 0.00018 25.2 0.5 27 33-62 1-27 (73)
80 cd07155 NR_DBD_ER_like DNA-bin 46.1 7 0.00015 25.8 0.1 27 33-62 1-27 (75)
81 cd07179 2DBD_NR_DBD2 The secon 46.0 8.6 0.00019 25.3 0.5 27 33-62 1-27 (74)
82 smart00290 ZnF_UBP Ubiquitin C 45.9 16 0.00034 21.6 1.6 22 32-53 1-22 (50)
83 cd06969 NR_DBD_NGFI-B DNA-bind 45.4 12 0.00027 24.6 1.2 28 32-62 2-29 (75)
84 cd07165 NR_DBD_DmE78_like DNA- 45.0 8 0.00017 25.9 0.2 27 33-62 1-27 (81)
85 PF00105 zf-C4: Zinc finger, C 44.5 8.6 0.00019 24.7 0.3 28 31-61 1-28 (70)
86 PF06677 Auto_anti-p27: Sjogre 44.5 11 0.00025 22.2 0.8 24 30-56 17-40 (41)
87 cd07154 NR_DBD_PNR_like The DN 43.3 14 0.0003 24.1 1.2 27 33-62 1-27 (73)
88 smart00399 ZnF_C4 c4 zinc fing 42.7 12 0.00026 24.1 0.8 27 33-62 2-28 (70)
89 PF08792 A2L_zn_ribbon: A2L zi 42.7 16 0.00034 20.6 1.2 29 30-60 3-31 (33)
90 PF08274 PhnA_Zn_Ribbon: PhnA 42.6 16 0.00034 20.2 1.1 24 32-58 4-27 (30)
91 PF03604 DNA_RNApol_7kD: DNA d 42.4 11 0.00024 21.1 0.6 23 32-57 2-24 (32)
92 cd00202 ZnF_GATA Zinc finger D 42.2 11 0.00024 23.5 0.5 33 32-64 1-35 (54)
93 PF13453 zf-TFIIB: Transcripti 42.0 22 0.00047 20.5 1.8 29 32-60 1-29 (41)
94 cd06959 NR_DBD_EcR_like The DN 41.7 11 0.00024 24.6 0.5 27 33-62 2-28 (73)
95 KOG3362|consensus 41.0 12 0.00025 28.4 0.6 34 28-62 116-150 (156)
96 PRK00420 hypothetical protein; 40.9 53 0.0012 23.6 4.0 28 30-60 23-50 (112)
97 cd06961 NR_DBD_TR DNA-binding 40.8 9.4 0.0002 25.9 0.1 27 33-62 2-28 (85)
98 cd07164 NR_DBD_PNR_like_1 DNA- 39.7 13 0.00029 24.6 0.7 27 33-62 1-27 (78)
99 COG0675 Transposase and inacti 39.6 17 0.00037 29.0 1.4 25 28-59 307-331 (364)
100 smart00661 RPOL9 RNA polymeras 38.0 27 0.00059 20.6 1.9 32 31-62 1-32 (52)
101 KOG4215|consensus 37.7 15 0.00032 32.0 0.8 32 28-62 17-48 (432)
102 PHA02942 putative transposase; 37.2 23 0.00049 30.5 1.9 28 29-59 324-351 (383)
103 TIGR00100 hypA hydrogenase nic 37.1 24 0.00051 25.2 1.7 30 27-60 67-96 (115)
104 smart00834 CxxC_CXXC_SSSS Puta 36.6 14 0.00031 20.8 0.4 27 32-58 7-34 (41)
105 cd07167 NR_DBD_Lrh-1_like The 35.8 13 0.00028 25.8 0.1 27 33-62 1-27 (93)
106 TIGR01384 TFS_arch transcripti 35.7 31 0.00068 23.6 2.1 31 30-60 62-100 (104)
107 PF14471 DUF4428: Domain of un 35.1 12 0.00026 23.1 -0.1 43 32-75 1-45 (51)
108 PRK04059 rpl34e 50S ribosomal 33.4 23 0.0005 24.5 1.1 31 28-58 32-79 (88)
109 PF01927 Mut7-C: Mut7-C RNAse 33.3 41 0.00088 24.8 2.5 32 28-59 89-133 (147)
110 TIGR00598 rad14 DNA repair pro 33.2 7.8 0.00017 30.0 -1.4 28 33-60 1-29 (172)
111 PF14376 Haem_bd: Haem-binding 32.9 22 0.00049 26.1 1.0 15 30-44 41-55 (137)
112 PRK00432 30S ribosomal protein 32.8 31 0.00067 21.1 1.5 26 29-57 19-44 (50)
113 PTZ00074 60S ribosomal protein 31.8 22 0.00047 26.6 0.8 31 28-58 39-86 (135)
114 TIGR02605 CxxC_CxxC_SSSS putat 30.8 21 0.00045 21.4 0.5 27 32-58 7-34 (52)
115 PRK03988 translation initiatio 30.4 91 0.002 23.1 3.9 42 11-58 89-131 (138)
116 KOG4846|consensus 30.2 22 0.00048 31.5 0.7 28 31-61 133-160 (538)
117 PF04161 Arv1: Arv1-like famil 29.8 26 0.00056 27.4 1.0 27 32-58 2-32 (208)
118 PRK06266 transcription initiat 29.6 13 0.00027 28.7 -0.8 31 31-62 118-148 (178)
119 PF13119 DUF3973: Domain of un 29.5 20 0.00043 21.2 0.2 14 51-64 2-15 (41)
120 PF12156 ATPase-cat_bd: Putati 29.3 23 0.00049 24.1 0.5 31 32-62 2-38 (88)
121 KOG4217|consensus 29.0 20 0.00042 32.3 0.2 30 28-60 267-296 (605)
122 TIGR00373 conserved hypothetic 28.7 14 0.0003 27.9 -0.7 30 31-61 110-139 (158)
123 PRK03681 hypA hydrogenase nick 28.6 25 0.00053 25.1 0.6 32 27-61 67-98 (114)
124 KOG1597|consensus 28.6 44 0.00094 28.2 2.1 29 32-60 2-31 (308)
125 PF06689 zf-C4_ClpX: ClpX C4-t 28.5 40 0.00086 19.6 1.4 29 31-59 2-33 (41)
126 PF00641 zf-RanBP: Zn-finger i 28.1 20 0.00044 19.1 0.1 16 26-41 14-29 (30)
127 COG1405 SUA7 Transcription ini 27.7 42 0.00091 27.9 1.9 28 32-60 3-30 (285)
128 PF01199 Ribosomal_L34e: Ribos 27.3 18 0.00039 25.3 -0.3 29 29-57 40-85 (94)
129 PF13462 Thioredoxin_4: Thiore 27.2 16 0.00034 26.1 -0.6 28 37-64 8-35 (162)
130 TIGR00382 clpX endopeptidase C 27.2 30 0.00064 30.2 1.0 30 30-59 7-38 (413)
131 PTZ00255 60S ribosomal protein 26.8 94 0.002 21.6 3.2 32 27-60 33-64 (90)
132 PRK12336 translation initiatio 26.6 99 0.0022 24.2 3.7 33 30-63 98-131 (201)
133 PF04170 NlpE: NlpE N-terminal 26.5 28 0.00061 23.4 0.6 16 48-63 2-17 (87)
134 KOG3408|consensus 25.9 24 0.00051 26.0 0.1 44 47-90 54-106 (129)
135 PRK00564 hypA hydrogenase nick 25.8 27 0.00058 25.0 0.4 30 28-60 69-98 (117)
136 PF07762 DUF1618: Protein of u 25.3 33 0.00071 24.3 0.8 15 43-57 1-15 (131)
137 PF04770 ZF-HD_dimer: ZF-HD pr 24.3 42 0.00091 21.6 1.0 29 34-63 23-52 (60)
138 PTZ00218 40S ribosomal protein 24.2 31 0.00068 21.7 0.4 29 28-58 14-42 (54)
139 PF10058 DUF2296: Predicted in 23.7 88 0.0019 19.4 2.4 40 19-58 4-52 (54)
140 smart00440 ZnF_C2C2 C2C2 Zinc 23.6 75 0.0016 18.3 2.0 27 32-58 2-36 (40)
141 PF13248 zf-ribbon_3: zinc-rib 23.3 39 0.00085 17.6 0.6 11 28-38 14-24 (26)
142 COG1592 Rubrerythrin [Energy p 23.3 1.2E+02 0.0025 23.4 3.4 34 12-62 113-146 (166)
143 PF02148 zf-UBP: Zn-finger in 22.6 40 0.00086 21.2 0.7 23 33-55 1-24 (63)
144 PF04810 zf-Sec23_Sec24: Sec23 22.3 60 0.0013 18.7 1.4 27 32-58 4-32 (40)
145 PF11261 IRF-2BP1_2: Interfero 22.3 22 0.00047 22.3 -0.6 30 30-59 3-33 (54)
146 COG2203 FhlA FOG: GAF domain [ 22.1 1.2E+02 0.0026 20.3 3.1 26 77-102 142-167 (175)
147 PRK12380 hydrogenase nickel in 21.9 44 0.00096 23.7 0.9 30 27-60 67-96 (113)
148 TIGR00311 aIF-2beta translatio 21.8 73 0.0016 23.5 2.0 30 30-59 97-127 (133)
149 PF01873 eIF-5_eIF-2B: Domain 20.8 67 0.0014 23.4 1.6 42 12-59 81-123 (125)
150 PF09723 Zn-ribbon_8: Zinc rib 20.7 37 0.0008 19.8 0.2 27 32-58 7-34 (42)
151 smart00336 BBOX B-Box-type zin 20.5 91 0.002 17.1 1.9 32 30-61 3-35 (42)
152 PRK03824 hypA hydrogenase nick 20.3 86 0.0019 22.9 2.2 27 49-75 106-133 (135)
153 smart00782 PhnA_Zn_Ribbon PhnA 20.1 60 0.0013 19.7 1.1 29 30-58 7-44 (47)
No 1
>KOG0703|consensus
Probab=100.00 E-value=1.6e-46 Score=305.61 Aligned_cols=121 Identities=57% Similarity=1.092 Sum_probs=116.6
Q ss_pred HHHHHHHHHHHHHhcCCCCCCccCCCCCCCCeeecccceeeecccccccccCCCccceeeecccCCCCHHHHHHHHhhcc
Q psy5674 12 QIQDKCQNLLMQMLKDDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDTWTPEQVVSLQQMGN 91 (145)
Q Consensus 12 ~~~e~~~~~l~~l~~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~w~~~~i~~l~~~GN 91 (145)
...+.++..|++||+.|+|++|||||+++|.|||+|+|||||+.|+||||+||+|||+|||++||.|++|+|+.|+..||
T Consensus 7 ~~~~~~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~GN 86 (287)
T KOG0703|consen 7 GSNERNKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMGN 86 (287)
T ss_pred cccchHHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHcc
Confidence 34566788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhCCCCCCCCCCchHHHHHHHHHHhhcccccCC
Q psy5674 92 SRARAVYEANIPDNFRRPQTDSTLEAFIRAKYEQKKYIASE 132 (145)
Q Consensus 92 ~~~n~~~e~~~p~~~~~p~~~~~~~~fI~~KY~~k~f~~~~ 132 (145)
.+||++||+.+|+.+.+|.++..+|+|||+||+.++|+.+.
T Consensus 87 ~~an~~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~~ 127 (287)
T KOG0703|consen 87 AKANSYYEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLDPE 127 (287)
T ss_pred hhhhhhccccCCccccCCChHHHHHHHHHHHHhhhhhccch
Confidence 99999999999999999999999999999999999999975
No 2
>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=100.00 E-value=3.6e-43 Score=254.14 Aligned_cols=113 Identities=51% Similarity=0.970 Sum_probs=91.1
Q ss_pred HHHHHHhcCCCCCCccCCCCCCCCeeecccceeeecccccccccCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHH
Q psy5674 19 NLLMQMLKDDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDTWTPEQVVSLQQMGNSRARAVY 98 (145)
Q Consensus 19 ~~l~~l~~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~w~~~~i~~l~~~GN~~~n~~~ 98 (145)
++|+.|++.|+|++|||||+++|+|||++||||||+.|+|+||.||+|+|+||||+||+|++++|+.|+.+||..+|++|
T Consensus 2 ~~l~~l~~~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~~GN~~~n~~~ 81 (116)
T PF01412_consen 2 KILRELLKKPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMREGGNKRANSIW 81 (116)
T ss_dssp HHHHHHHCSTTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHHSHHHHHHHHH
T ss_pred HHHHHHHcCcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHHHChHHHHHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhCCCCCCCCC--CchHHHHHHHHHHhhcccccC
Q psy5674 99 EANIPDNFRRPQ--TDSTLEAFIRAKYEQKKYIAS 131 (145)
Q Consensus 99 e~~~p~~~~~p~--~~~~~~~fI~~KY~~k~f~~~ 131 (145)
|++.+.....|. +...+++||++||++++|+.+
T Consensus 82 e~~~~~~~~~~~~~~~~~~~~fI~~KY~~k~f~~~ 116 (116)
T PF01412_consen 82 EANSPPPKKPPPSSDQEKREQFIRAKYVEKAFISK 116 (116)
T ss_dssp TTTSTTTTTHCTTSHHHHHHHHHHHHHTTHTTS-C
T ss_pred HcCCCCCCCCCCCCcHHHHHHHHHHHHHhhhhccC
Confidence 999443333222 234579999999999999864
No 3
>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=100.00 E-value=1.8e-41 Score=244.07 Aligned_cols=107 Identities=50% Similarity=0.919 Sum_probs=98.2
Q ss_pred CCCCCccCCCCCCCCeeecccceeeecccccccccCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHHHhhCCCCCC
Q psy5674 28 DDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDTWTPEQVVSLQQMGNSRARAVYEANIPDNFR 107 (145)
Q Consensus 28 p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~w~~~~i~~l~~~GN~~~n~~~e~~~p~~~~ 107 (145)
|+|++|||||+++|+|||++||||||+.|+|+||.||+|||+||||+||+|++++|++|+.+||.++|++||+++++...
T Consensus 1 ~~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~w~~~~i~~~~~~GN~~~n~~~e~~~~~~~~ 80 (112)
T smart00105 1 PGNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTWTEEELRLLQKGGNENANSIWESNLDDFSL 80 (112)
T ss_pred CCCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCCCCHHHHHHHHHhhhHHHHHHHHhhCCcccc
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999987654
Q ss_pred CCC---CchHHHHHHHHHHhhcccccCCCC
Q psy5674 108 RPQ---TDSTLEAFIRAKYEQKKYIASEWV 134 (145)
Q Consensus 108 ~p~---~~~~~~~fI~~KY~~k~f~~~~~~ 134 (145)
+|. ....+++||+.||++++|+.....
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~~ 110 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPESA 110 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhccccccC
Confidence 432 235579999999999999987653
No 4
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=5.9e-38 Score=272.42 Aligned_cols=129 Identities=34% Similarity=0.627 Sum_probs=112.7
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHhcCCCCCCccCCCCCCCCeeecccceeeecccccccccCCCccceeeecccCCCCH
Q psy5674 1 MSSKAEKERQKQIQDKCQNLLMQMLKDDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDTWTP 80 (145)
Q Consensus 1 ~~~~~~~~~~k~~~e~~~~~l~~l~~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~w~~ 80 (145)
|.|+.++|| ++++|++|++.|+|+.|+|||+.+|+|||++||||||+.|+||||.|| +|||||+||+|++
T Consensus 1 M~SKR~qER-------nekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDkWT~ 70 (648)
T PLN03119 1 MGSKREEER-------NEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSKFTS 70 (648)
T ss_pred CcchHHHHH-------HHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCCCCH
Confidence 666665554 557899999999999999999999999999999999999999999998 5999999999999
Q ss_pred HHHHHHHhhccHHHHHHHHhhCCCCCCC-CC--CchHHHHHHHHHHhhcccccCCCCCCCCC
Q psy5674 81 EQVVSLQQMGNSRARAVYEANIPDNFRR-PQ--TDSTLEAFIRAKYEQKKYIASEWVPPVLP 139 (145)
Q Consensus 81 ~~i~~l~~~GN~~~n~~~e~~~p~~~~~-p~--~~~~~~~fI~~KY~~k~f~~~~~~~~~~~ 139 (145)
++|++|+.+||.++|+|||++|+....+ |. +...+++||+.||++|+|+.....+.+++
T Consensus 71 EEVe~Mk~gGN~~AN~iyeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~~~d~p~~ 132 (648)
T PLN03119 71 KEVEVLQNGGNQRAREIYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGANDADKPSK 132 (648)
T ss_pred HHHHHHHHhchHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcCCCCCCcc
Confidence 9999999999999999999999875433 33 23457899999999999999887765554
No 5
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=1.5e-37 Score=271.64 Aligned_cols=129 Identities=33% Similarity=0.622 Sum_probs=112.0
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHhcCCCCCCccCCCCCCCCeeecccceeeecccccccccCCCccceeeecccCCCCH
Q psy5674 1 MSSKAEKERQKQIQDKCQNLLMQMLKDDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDTWTP 80 (145)
Q Consensus 1 ~~~~~~~~~~k~~~e~~~~~l~~l~~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~w~~ 80 (145)
|.||.++|+. +++|++|++.|+|+.|+|||+++|+|||++||||||+.|+||||.|| ++||||+||+|++
T Consensus 1 m~SkkqqErn-------ekiLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLg---hRVKSVTLD~Wtd 70 (705)
T PLN03131 1 MGSRKEEERN-------EKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFT---HRVKSVSMSKFTS 70 (705)
T ss_pred CcchHHHHHH-------HHHHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchhhhcccC---cccccccCCCCCH
Confidence 6666655554 46899999999999999999999999999999999999999999997 5999999999999
Q ss_pred HHHHHHHhhccHHHHHHHHhhCCCCC-CCCCC--chHHHHHHHHHHhhcccccCCCCCCCCC
Q psy5674 81 EQVVSLQQMGNSRARAVYEANIPDNF-RRPQT--DSTLEAFIRAKYEQKKYIASEWVPPVLP 139 (145)
Q Consensus 81 ~~i~~l~~~GN~~~n~~~e~~~p~~~-~~p~~--~~~~~~fI~~KY~~k~f~~~~~~~~~~~ 139 (145)
++|+.|+.+||.++|+|||++|+... ..|.. ...+++||+.||++|+|+.....+.++.
T Consensus 71 eEV~~Mk~gGN~~AN~iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~~s~d~ppr 132 (705)
T PLN03131 71 QDVEALQNGGNQRAREIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGGKTHDKPPR 132 (705)
T ss_pred HHHHHHHHhccHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcCCCCCCCch
Confidence 99999999999999999999997653 23332 2447899999999999999886665543
No 6
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=100.00 E-value=2.4e-37 Score=256.51 Aligned_cols=118 Identities=48% Similarity=0.876 Sum_probs=103.8
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCCCeeecccceeeecccccccccCCCccceeeecccCCCCHHHHHHHHhhccHHHHHH
Q psy5674 18 QNLLMQMLKDDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDTWTPEQVVSLQQMGNSRARAV 97 (145)
Q Consensus 18 ~~~l~~l~~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~w~~~~i~~l~~~GN~~~n~~ 97 (145)
+.++..|...++|+.|||||+++|+|+|++||||||++||||||+||+||++||||+||+|++++|++|..+||.+||.|
T Consensus 8 ~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a~~~ 87 (319)
T COG5347 8 RKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNANRF 87 (319)
T ss_pred HHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhhhhH
Confidence 34666777889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCCCCCCCC---C-CchHHHHHHHHHHhhcccccCCCCC
Q psy5674 98 YEANIPDNFRRP---Q-TDSTLEAFIRAKYEQKKYIASEWVP 135 (145)
Q Consensus 98 ~e~~~p~~~~~p---~-~~~~~~~fI~~KY~~k~f~~~~~~~ 135 (145)
|+.++-.....| . ++..+++||++||+.++|+.....+
T Consensus 88 ~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~~~~ 129 (319)
T COG5347 88 YEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDSSSP 129 (319)
T ss_pred hccCCCcccccccccccCHHHHHHHHHHHHHhhhccccccCc
Confidence 998875532122 2 3455799999999999999865444
No 7
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.97 E-value=2.1e-31 Score=221.83 Aligned_cols=123 Identities=39% Similarity=0.670 Sum_probs=100.4
Q ss_pred HHHHHHhcCCCCCCccCCCCCCCCeeecccceeeecccccccccCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHH
Q psy5674 19 NLLMQMLKDDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDTWTPEQVVSLQQMGNSRARAVY 98 (145)
Q Consensus 19 ~~l~~l~~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~w~~~~i~~l~~~GN~~~n~~~ 98 (145)
.+|++|+..|+|+.|+|||+++|+|+|++||||||+.|+|+||.||+||++|||++||+|++++|++|+.+||.++|.||
T Consensus 11 ~vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~~fF 90 (395)
T PLN03114 11 SVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQVFF 90 (395)
T ss_pred HHHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhCCCCCCCCC-----CchHHHHHHHHHHhhcccccCCC-CCCCCCCC
Q psy5674 99 EANIPDNFRRPQ-----TDSTLEAFIRAKYEQKKYIASEW-VPPVLPKN 141 (145)
Q Consensus 99 e~~~p~~~~~p~-----~~~~~~~fI~~KY~~k~f~~~~~-~~~~~~~~ 141 (145)
+...-.....+. .....-.-+.++++.+.+..... .|+.+|+.
T Consensus 91 ~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~~a~~~~~~p~~~~~~ 139 (395)
T PLN03114 91 KQYGWSDGGKTEAKYTSRAADLYKQILAKEVAKSKAEEELDLPPSPPDS 139 (395)
T ss_pred HHcCCCCCCCcccccCCHHHHHHHHHHHHHHHHhhhccccCCCCCCCCc
Confidence 865322111111 11222344888999998886654 44444443
No 8
>KOG0705|consensus
Probab=99.97 E-value=7.8e-31 Score=228.33 Aligned_cols=115 Identities=43% Similarity=0.807 Sum_probs=103.8
Q ss_pred HHHHHhcCCCCCCccCCCCCCCCeeecccceeeecccccccccCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHHH
Q psy5674 20 LLMQMLKDDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDTWTPEQVVSLQQMGNSRARAVYE 99 (145)
Q Consensus 20 ~l~~l~~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~w~~~~i~~l~~~GN~~~n~~~e 99 (145)
.|..+..-+||..|+||++++|.|||+|+|+++|++|+||||.||+|+|+|+||.||.|..|.+..|..+||+.||.+||
T Consensus 503 a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~vWE 582 (749)
T KOG0705|consen 503 ALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANSVWE 582 (749)
T ss_pred HHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHHHhh
Confidence 34455567999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCCCCCCCCchH---HHHHHHHHHhhcccccCCCCC
Q psy5674 100 ANIPDNFRRPQTDST---LEAFIRAKYEQKKYIASEWVP 135 (145)
Q Consensus 100 ~~~p~~~~~p~~~~~---~~~fI~~KY~~k~f~~~~~~~ 135 (145)
..+ .+..+|++++. +|.||++||++|.|.......
T Consensus 583 ~~~-~G~~KPs~~s~REEkErwIr~KYeqklFLaPl~~t 620 (749)
T KOG0705|consen 583 GSS-QGQTKPSPDSSREEKERWIRAKYEQKLFLAPLPCT 620 (749)
T ss_pred hhc-cCCcCCCccccHHHHHHHHHHHHHHHhhcCCCCCC
Confidence 844 56678888765 478999999999999876554
No 9
>KOG0704|consensus
Probab=99.96 E-value=2.9e-30 Score=213.91 Aligned_cols=124 Identities=31% Similarity=0.610 Sum_probs=92.7
Q ss_pred HHHHHhcCCCCCCccCCCCCCCCeeecccceeeecccccccccCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHHH
Q psy5674 20 LLMQMLKDDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDTWTPEQVVSLQQMGNSRARAVYE 99 (145)
Q Consensus 20 ~l~~l~~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~w~~~~i~~l~~~GN~~~n~~~e 99 (145)
.|.+|....+|+.|+||++++|+|||++||||||++|+|+||.||+|||+|||||||+|.+.||+.|+++||.++++|++
T Consensus 9 ~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~~eFL~ 88 (386)
T KOG0704|consen 9 VLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERFREFLS 88 (386)
T ss_pred HHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhHHHHHh
Confidence 44445555699999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred hhCCCCCCCC------CC-chHHHHHHHHHHhhcccccCCCCCCCCCCCCC
Q psy5674 100 ANIPDNFRRP------QT-DSTLEAFIRAKYEQKKYIASEWVPPVLPKNSF 143 (145)
Q Consensus 100 ~~~p~~~~~p------~~-~~~~~~fI~~KY~~k~f~~~~~~~~~~~~~~~ 143 (145)
..-.-...-| +. .+..++=|.+-=+-+.|-....+..+.|+-+|
T Consensus 89 s~~~~~e~~~i~eKYns~aAa~yRdki~~laegr~w~d~~~~k~~~p~~sy 139 (386)
T KOG0704|consen 89 SQGIYKETWPIREKYNSRAAALYRDKIAALAEGREWNDPPYLKEDNPAQSY 139 (386)
T ss_pred hCccccccccHHHhhccHHHHHHHHHHHHHhcCCcccccccccccCccccc
Confidence 5432111111 11 12234555555555555444445555554443
No 10
>KOG0706|consensus
Probab=99.96 E-value=2.7e-30 Score=219.37 Aligned_cols=85 Identities=48% Similarity=0.903 Sum_probs=81.9
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCeeecccceeeecccccccccCCCccceeeecccCCCCHHHHHHHHhhccHHHHH
Q psy5674 17 CQNLLMQMLKDDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDTWTPEQVVSLQQMGNSRARA 96 (145)
Q Consensus 17 ~~~~l~~l~~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~w~~~~i~~l~~~GN~~~n~ 96 (145)
.+..++.|...+.|++|+|||+++|+|+|++||||||++|+++||.||+||++|||..||+|+..+|+.|+.+||.+|+.
T Consensus 10 ~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~ 89 (454)
T KOG0706|consen 10 IQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARV 89 (454)
T ss_pred HHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHH
Confidence 45689999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhh
Q psy5674 97 VYEAN 101 (145)
Q Consensus 97 ~~e~~ 101 (145)
|+...
T Consensus 90 FFkqh 94 (454)
T KOG0706|consen 90 FFKQH 94 (454)
T ss_pred HHHHc
Confidence 99865
No 11
>KOG0521|consensus
Probab=99.93 E-value=1e-26 Score=211.41 Aligned_cols=116 Identities=39% Similarity=0.804 Sum_probs=104.8
Q ss_pred HHHHHhcCCCCCCccCCCCCCCCeeecccceeeecccccccccCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHHH
Q psy5674 20 LLMQMLKDDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDTWTPEQVVSLQQMGNSRARAVYE 99 (145)
Q Consensus 20 ~l~~l~~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~w~~~~i~~l~~~GN~~~n~~~e 99 (145)
.+..+...|||..|+|||++.|+|+|+|+||.+|++|+|+||.||+|+|+|+||+||.|.++.+.+++.+||..+|.+||
T Consensus 416 ~~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e 495 (785)
T KOG0521|consen 416 VIEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYE 495 (785)
T ss_pred hhhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhh
Confidence 36677788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCC-CCCCCC---chHHHHHHHHHHhhcccccCCCCC
Q psy5674 100 ANIPDN-FRRPQT---DSTLEAFIRAKYEQKKYIASEWVP 135 (145)
Q Consensus 100 ~~~p~~-~~~p~~---~~~~~~fI~~KY~~k~f~~~~~~~ 135 (145)
+.+++. ..+|++ ...++.||++||++++|.-+....
T Consensus 496 ~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~~ 535 (785)
T KOG0521|consen 496 ALLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQI 535 (785)
T ss_pred cccccccccCCCCccchhhhhHhhhcccceeeEeecccch
Confidence 999864 455543 345789999999999998876655
No 12
>KOG0818|consensus
Probab=99.89 E-value=3.7e-24 Score=184.43 Aligned_cols=108 Identities=31% Similarity=0.649 Sum_probs=96.8
Q ss_pred cCCCCCCccCCCCCCCCeeecccceeeecccccccccCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHHHhhCCCC
Q psy5674 26 KDDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDTWTPEQVVSLQQMGNSRARAVYEANIPDN 105 (145)
Q Consensus 26 ~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~w~~~~i~~l~~~GN~~~n~~~e~~~p~~ 105 (145)
.....++|+|||+++|.|+|++-|+|+|.+|..+||.||.|||.||+|....|.+..|++...+.|..+|.|||..|-++
T Consensus 4 ~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld~ 83 (669)
T KOG0818|consen 4 RLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLDP 83 (669)
T ss_pred cchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccCc
Confidence 34567899999999999999999999999999999999999999999999999999999999999999999999998663
Q ss_pred ------CCCCCCchH----HHHHHHHHHhhcccccCCC
Q psy5674 106 ------FRRPQTDST----LEAFIRAKYEQKKYIASEW 133 (145)
Q Consensus 106 ------~~~p~~~~~----~~~fI~~KY~~k~f~~~~~ 133 (145)
.++|++.+. .++||++||+...|+.+..
T Consensus 84 st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~~~~ 121 (669)
T KOG0818|consen 84 ATIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVHRLP 121 (669)
T ss_pred hhhhcccCCCCCcCCCCccHHHHHHHHHHheeeeccCC
Confidence 345666543 5899999999999998543
No 13
>KOG1117|consensus
Probab=99.84 E-value=1.9e-21 Score=175.40 Aligned_cols=110 Identities=35% Similarity=0.712 Sum_probs=98.4
Q ss_pred HHHhcCCCCCCccCCCCCCCCeeecccceeeecccccccccCCCccceeeecccCC--CCHHHHHHHHhhccHHHHHHHH
Q psy5674 22 MQMLKDDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDT--WTPEQVVSLQQMGNSRARAVYE 99 (145)
Q Consensus 22 ~~l~~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~--w~~~~i~~l~~~GN~~~n~~~e 99 (145)
.++.....|+.|+|||++.|.|||+|++|.+|-.|+|-||++|..+|+|+|++||. |+.+-|+++..+||.++|+||.
T Consensus 290 eriW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fwa 369 (1186)
T KOG1117|consen 290 ERIWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFWA 369 (1186)
T ss_pred HHHHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCcccccccc
Confidence 35666789999999999999999999999999999999999999999999999995 9999999999999999999999
Q ss_pred hhCCCCCCC-C-CCchHHHHHHHHHHhhcccccC
Q psy5674 100 ANIPDNFRR-P-QTDSTLEAFIRAKYEQKKYIAS 131 (145)
Q Consensus 100 ~~~p~~~~~-p-~~~~~~~~fI~~KY~~k~f~~~ 131 (145)
+++|.+.-. | .+-+.+++||..||.+.+|...
T Consensus 370 ~nl~~~e~lh~dssp~~r~~fi~~Kykeg~fRk~ 403 (1186)
T KOG1117|consen 370 GNLPPNEHLHPDSSPSTRRQFIKEKYKEGKFRKE 403 (1186)
T ss_pred cCCCCccccCCCCCcchhhhHHHHHhhccccccc
Confidence 999876432 2 2335689999999999998654
No 14
>KOG0702|consensus
Probab=99.70 E-value=1.6e-17 Score=143.08 Aligned_cols=119 Identities=24% Similarity=0.504 Sum_probs=102.4
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCccCCCCCCC-CeeecccceeeecccccccccCCCccceeeecccCCCCHHHHHHHHhh
Q psy5674 11 KQIQDKCQNLLMQMLKDDDNKYCVDCDAKGP-RWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDTWTPEQVVSLQQM 89 (145)
Q Consensus 11 k~~~e~~~~~l~~l~~~p~N~~CaDCg~~~p-~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~w~~~~i~~l~~~ 89 (145)
|+.++.++.+||+|++.|+|++|++|....+ +|+...-|-|+|..|+|+-|.|. .-+|||++.|.+++..|+..|+.+
T Consensus 6 ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~-~ahRvksiSmttft~qevs~lQsh 84 (524)
T KOG0702|consen 6 KEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLN-PAHRVKSISMTTFTDQEVSFLQSH 84 (524)
T ss_pred ccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCC-CccccceeeeeeccccchHHHhhc
Confidence 4456677999999999999999999999877 99999999999999999999985 468999999999999999999999
Q ss_pred ccHHHHHHHHhhCCCCC-CCCC--CchHHHHHHHHHHhhccccc
Q psy5674 90 GNSRARAVYEANIPDNF-RRPQ--TDSTLEAFIRAKYEQKKYIA 130 (145)
Q Consensus 90 GN~~~n~~~e~~~p~~~-~~p~--~~~~~~~fI~~KY~~k~f~~ 130 (145)
||....+||.+...... .-|. +-...++||+.||+.++|+-
T Consensus 85 gNq~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v 128 (524)
T KOG0702|consen 85 GNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYV 128 (524)
T ss_pred chhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeec
Confidence 99999999986654321 1232 23457999999999999965
No 15
>KOG0521|consensus
Probab=95.36 E-value=0.0032 Score=58.56 Aligned_cols=73 Identities=19% Similarity=0.224 Sum_probs=62.6
Q ss_pred CCCCCCccCCCCC-CCCeeecccceeeecccccccccCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHHHhh
Q psy5674 27 DDDNKYCVDCDAK-GPRWASWNIGIFLCIRCAGIHRNLGVHISRVKSVNLDTWTPEQVVSLQQMGNSRARAVYEAN 101 (145)
Q Consensus 27 ~p~N~~CaDCg~~-~p~w~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~ld~w~~~~i~~l~~~GN~~~n~~~e~~ 101 (145)
...+..|++|++. ...|+++++.+-+|..|+++|+..+.+++...++.|++..+ |......|+..++..+...
T Consensus 627 ~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~~g 700 (785)
T KOG0521|consen 627 ASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATASG 700 (785)
T ss_pred hccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhhhc
Confidence 3457889999985 78899999999999999999999999999999999999887 7777777777777766543
No 16
>PRK12495 hypothetical protein; Provisional
Probab=93.84 E-value=0.11 Score=41.69 Aligned_cols=37 Identities=22% Similarity=0.323 Sum_probs=28.6
Q ss_pred HHHHHhcC---CCCCCccCCCCCCCCeeecccceeeeccccccc
Q psy5674 20 LLMQMLKD---DDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 20 ~l~~l~~~---p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iH 60 (145)
.+-.||.+ ..+..|.+||.+-|.+ -|+.+|..|..+-
T Consensus 29 ~ma~lL~~gatmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 29 RMSELLLQGATMTNAHCDECGDPIFRH----DGQEFCPTCQQPV 68 (226)
T ss_pred HHHHHHHhhcccchhhcccccCcccCC----CCeeECCCCCCcc
Confidence 44445543 7899999999998832 7999999998764
No 17
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=91.32 E-value=0.17 Score=32.77 Aligned_cols=35 Identities=23% Similarity=0.408 Sum_probs=24.2
Q ss_pred cCCCCCCccCCCCCCCCe-eecccceeeeccccccc
Q psy5674 26 KDDDNKYCVDCDAKGPRW-ASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 26 ~~p~N~~CaDCg~~~p~w-~s~~~GvflC~~Cs~iH 60 (145)
..++...|.|||.+=|.= .-..-|+..|+.|...+
T Consensus 27 ~~~s~g~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 27 IGPSLRECEDCGEPIPEARREALPGVTRCVSCQEIL 62 (63)
T ss_pred cCCCCCeeccCCCcChHHHHhhcCCcCCcHHHHhhc
Confidence 457788999999984421 12335788999997654
No 18
>PRK11019 hypothetical protein; Provisional
Probab=89.79 E-value=0.18 Score=34.91 Aligned_cols=50 Identities=16% Similarity=0.292 Sum_probs=30.6
Q ss_pred HHHHHHHHHHhcCCCCCCccCCCCCCCC-eeecccceeeecccccccccCC
Q psy5674 15 DKCQNLLMQMLKDDDNKYCVDCDAKGPR-WASWNIGIFLCIRCAGIHRNLG 64 (145)
Q Consensus 15 e~~~~~l~~l~~~p~N~~CaDCg~~~p~-w~s~~~GvflC~~Cs~iHR~lg 64 (145)
...+.++.++...+.-..|.|||.+=|. =.-.-.++..|+.|...+...+
T Consensus 21 ~aI~~a~~r~~~g~syg~C~~CG~~Ip~~Rl~A~P~a~~Cv~Cq~~~E~~~ 71 (88)
T PRK11019 21 DAIARARSELPRGESLTECEECGEPIPEARRKAIPGVRLCVACQQEKDLQQ 71 (88)
T ss_pred HHHHHHHhhcccCCcCCeeCcCCCcCcHHHHhhcCCccccHHHHHHHHHHH
Confidence 3334444444343456799999998442 1122347889999999875443
No 19
>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=88.39 E-value=0.36 Score=28.56 Aligned_cols=28 Identities=21% Similarity=0.445 Sum_probs=21.8
Q ss_pred CccCCCCCCCCeeecccceeeeccccccc
Q psy5674 32 YCVDCDAKGPRWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~GvflC~~Cs~iH 60 (145)
+|..||+.. .-.....|-++|..|..+-
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BBE
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCEe
Confidence 699999977 4556779999999996553
No 20
>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=88.35 E-value=0.17 Score=29.10 Aligned_cols=27 Identities=19% Similarity=0.482 Sum_probs=16.9
Q ss_pred CCccCCCCC-CCCeeecccceeeecccc
Q psy5674 31 KYCVDCDAK-GPRWASWNIGIFLCIRCA 57 (145)
Q Consensus 31 ~~CaDCg~~-~p~w~s~~~GvflC~~Cs 57 (145)
..|.+||.+ .-+|..-+|+.-||..|.
T Consensus 4 ~~C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp EE-TTT--EES-SSCCCCTS-S--TTT-
T ss_pred chHhHhCCHHHHHHHHHhCCcccccccc
Confidence 469999997 677999999999999994
No 21
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=87.95 E-value=0.42 Score=27.65 Aligned_cols=34 Identities=15% Similarity=0.243 Sum_probs=29.1
Q ss_pred CCCCccCCCCCCCCeeecccceeeecccccc-ccc
Q psy5674 29 DNKYCVDCDAKGPRWASWNIGIFLCIRCAGI-HRN 62 (145)
Q Consensus 29 ~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~i-HR~ 62 (145)
.+..|..|+.....+...+=++++|..|... |+.
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCCC
Confidence 3678999998888899999999999999988 876
No 22
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=87.53 E-value=0.39 Score=32.01 Aligned_cols=34 Identities=21% Similarity=0.475 Sum_probs=22.9
Q ss_pred CCCCccCCCCCCCC-eeecccceeeeccccccccc
Q psy5674 29 DNKYCVDCDAKGPR-WASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 29 ~N~~CaDCg~~~p~-w~s~~~GvflC~~Cs~iHR~ 62 (145)
+...|.|||.+=|. =.-.--|+..|+.|...+-.
T Consensus 33 ~~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~E~ 67 (73)
T PRK13715 33 PVYLCEACGNPIPEARRKIFPGVTLCVECQAYQER 67 (73)
T ss_pred CcccHhhcCCcCCHHHHhcCCCcCCCHHHHHHHHH
Confidence 34689999998442 11223588999999876543
No 23
>PHA00080 DksA-like zinc finger domain containing protein
Probab=85.38 E-value=0.69 Score=30.72 Aligned_cols=35 Identities=20% Similarity=0.397 Sum_probs=23.7
Q ss_pred CCCCCCccCCCCCCCC-eeecccceeeecccccccc
Q psy5674 27 DDDNKYCVDCDAKGPR-WASWNIGIFLCIRCAGIHR 61 (145)
Q Consensus 27 ~p~N~~CaDCg~~~p~-w~s~~~GvflC~~Cs~iHR 61 (145)
.++...|.|||.+=|. =.-..-++..|+.|...+-
T Consensus 28 ~~~~~~C~~Cg~~Ip~~Rl~a~P~~~~Cv~Cq~~~E 63 (72)
T PHA00080 28 APSATHCEECGDPIPEARREAVPGCRTCVSCQEILE 63 (72)
T ss_pred CCCCCEecCCCCcCcHHHHHhCCCccCcHHHHHHHH
Confidence 4667799999997331 1112347788999988653
No 24
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=84.67 E-value=0.3 Score=35.65 Aligned_cols=32 Identities=22% Similarity=0.382 Sum_probs=21.4
Q ss_pred CCCccCCCCCCC-Ceeecccceeeecccccccc
Q psy5674 30 NKYCVDCDAKGP-RWASWNIGIFLCIRCAGIHR 61 (145)
Q Consensus 30 N~~CaDCg~~~p-~w~s~~~GvflC~~Cs~iHR 61 (145)
=.+|.+||.+=| .=.-.--+..+|+.|...|-
T Consensus 80 YG~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~E 112 (120)
T COG1734 80 YGICEECGEPIPEARLEARPTARLCIECQERAE 112 (120)
T ss_pred ccchhccCCcCCHHHHhhCcchHHHHHHHHHHH
Confidence 348999999832 11222346789999988764
No 25
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=84.31 E-value=5.7 Score=28.37 Aligned_cols=56 Identities=13% Similarity=0.323 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHH-HHHHHHHhcCC----CCCCccCCCCC-----CCCeeecccceeeeccccccc
Q psy5674 5 AEKERQKQIQDKC-QNLLMQMLKDD----DNKYCVDCDAK-----GPRWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 5 ~~~~~~k~~~e~~-~~~l~~l~~~p----~N~~CaDCg~~-----~p~w~s~~~GvflC~~Cs~iH 60 (145)
.|++|-++|.+.. +...+.-.... +...|+-|+.+ ++.-.+.+-.--||..|...+
T Consensus 24 ~E~~Ri~kLk~~L~~e~~r~~~~~~~~~~~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~ 89 (118)
T PF02318_consen 24 KEEERIRKLKQELQKEKMRREALGNSQKYGERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYS 89 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCSCSTTHCCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEET
T ss_pred HHHHHHHHHHHHHHHHHHHhhccccccccCCcchhhhCCcccccCCCCCcCCcCCccccCccCCcC
Confidence 3455555555555 22334333334 78899999986 344456666777888887764
No 26
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=83.32 E-value=0.67 Score=36.65 Aligned_cols=32 Identities=31% Similarity=0.490 Sum_probs=27.3
Q ss_pred CCCCCccCCCCCCC-Ceeecccceeeecccccc
Q psy5674 28 DDNKYCVDCDAKGP-RWASWNIGIFLCIRCAGI 59 (145)
Q Consensus 28 p~N~~CaDCg~~~p-~w~s~~~GvflC~~Cs~i 59 (145)
|.-..|+-||.+.. .|.+...|.++|..|...
T Consensus 147 p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~~ 179 (247)
T PRK00085 147 LDLDHCAVCGAPGDHRYFSPKEGGAVCSECGDP 179 (247)
T ss_pred cchhhHhcCCCCCCceEEecccCCcccccccCc
Confidence 77789999998844 788999999999999733
No 27
>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=80.90 E-value=1.6 Score=34.32 Aligned_cols=33 Identities=27% Similarity=0.433 Sum_probs=27.5
Q ss_pred CCCCCCccCCCCCCC-Ceeecccceeeecccccc
Q psy5674 27 DDDNKYCVDCDAKGP-RWASWNIGIFLCIRCAGI 59 (145)
Q Consensus 27 ~p~N~~CaDCg~~~p-~w~s~~~GvflC~~Cs~i 59 (145)
.|.-..|+.||..++ .+.+...|.++|..|...
T Consensus 144 ~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 144 ALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred CcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 377789999998544 688999999999999764
No 28
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=77.54 E-value=2 Score=26.53 Aligned_cols=37 Identities=24% Similarity=0.550 Sum_probs=29.6
Q ss_pred CCCCccCCCCC-CCCeeecccce-eeecccccccccCCC
Q psy5674 29 DNKYCVDCDAK-GPRWASWNIGI-FLCIRCAGIHRNLGV 65 (145)
Q Consensus 29 ~N~~CaDCg~~-~p~w~s~~~Gv-flC~~Cs~iHR~lg~ 65 (145)
....|..|+.. .|.|=.-..|- +||-.|.--.+..+.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 46789999986 67788878886 999999887776553
No 29
>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=77.49 E-value=1.8 Score=24.92 Aligned_cols=28 Identities=29% Similarity=0.765 Sum_probs=23.3
Q ss_pred CCCCCccCCCCCCCCeeecccceeeeccccc
Q psy5674 28 DDNKYCVDCDAKGPRWASWNIGIFLCIRCAG 58 (145)
Q Consensus 28 p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~ 58 (145)
..|..|..|++. |...+-|-+.|..|..
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCce
Confidence 346679999998 8889999999999853
No 30
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=77.14 E-value=1.7 Score=32.85 Aligned_cols=45 Identities=24% Similarity=0.434 Sum_probs=28.0
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCC-Ceeecccceeeeccccccccc
Q psy5674 17 CQNLLMQMLKDDDNKYCVDCDAKGP-RWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 17 ~~~~l~~l~~~p~N~~CaDCg~~~p-~w~s~~~GvflC~~Cs~iHR~ 62 (145)
.+..|.+ +..+.-.+|-+||.+=| .=.-.--++..|+.|...+-.
T Consensus 99 I~~AL~R-i~~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~ 144 (151)
T PRK10778 99 IEKTLKK-VEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEI 144 (151)
T ss_pred HHHHHHH-HhCCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHH
Confidence 3334444 34578899999999721 111222356789999887654
No 31
>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=75.66 E-value=5.7 Score=23.65 Aligned_cols=38 Identities=18% Similarity=0.386 Sum_probs=25.8
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCCCeeecccceeeecccc
Q psy5674 18 QNLLMQMLKDDDNKYCVDCDAKGPRWASWNIGIFLCIRCA 57 (145)
Q Consensus 18 ~~~l~~l~~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs 57 (145)
.+.|.+ ++.|+.-+|..||+....++ -+.+.+-|..|.
T Consensus 7 ~~~l~~-~RW~~g~~CP~Cg~~~~~~~-~~~~~~~C~~C~ 44 (46)
T PF12760_consen 7 REYLEE-IRWPDGFVCPHCGSTKHYRL-KTRGRYRCKACR 44 (46)
T ss_pred HHHHHH-hcCCCCCCCCCCCCeeeEEe-CCCCeEECCCCC
Confidence 334433 45566688999999855433 337899999885
No 32
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=73.84 E-value=2 Score=34.69 Aligned_cols=30 Identities=33% Similarity=0.697 Sum_probs=26.9
Q ss_pred CCCCCccCCCCC-CCCeeecccceeeecccc
Q psy5674 28 DDNKYCVDCDAK-GPRWASWNIGIFLCIRCA 57 (145)
Q Consensus 28 p~N~~CaDCg~~-~p~w~s~~~GvflC~~Cs 57 (145)
|.=..|+.||++ ++...|.-.|-++|..|+
T Consensus 152 ~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 667889999998 557999999999999998
No 33
>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=73.74 E-value=1.6 Score=24.97 Aligned_cols=32 Identities=28% Similarity=0.690 Sum_probs=22.8
Q ss_pred ccCCCCC-CCCeeeccccee-eecccccccccCC
Q psy5674 33 CVDCDAK-GPRWASWNIGIF-LCIRCAGIHRNLG 64 (145)
Q Consensus 33 CaDCg~~-~p~w~s~~~Gvf-lC~~Cs~iHR~lg 64 (145)
|..|++. .|.|=....|-. ||..|.-.++..+
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~ 34 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYG 34 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhC
Confidence 8899986 789988888888 9999987766543
No 34
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=72.98 E-value=2.4 Score=32.23 Aligned_cols=45 Identities=11% Similarity=0.172 Sum_probs=27.3
Q ss_pred HHHHHHHHhcCCCCCCccCCCCC-CCCeeecccceeeeccccccccc
Q psy5674 17 CQNLLMQMLKDDDNKYCVDCDAK-GPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 17 ~~~~l~~l~~~p~N~~CaDCg~~-~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
.+..|.+|- ...=..|.+||.+ .+.=.-+.-++..|+.|+..+-.
T Consensus 74 Ie~AL~Ri~-~G~YG~Ce~CGe~I~~~RL~a~P~a~~Ci~Cq~~~E~ 119 (159)
T TIGR02890 74 IEHALQKIE-NGTYGICEVCGKPIPYERLEAIPTATTCVECQNRKEV 119 (159)
T ss_pred HHHHHHHHh-CCCCCeecccCCcccHHHHhhCCCcchhHHHHHHhhh
Confidence 344455553 3455689999987 21111223456799999887643
No 35
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=72.92 E-value=5 Score=32.87 Aligned_cols=38 Identities=18% Similarity=0.450 Sum_probs=29.1
Q ss_pred HHHHHHHHhc-CCCCCCccCCCCCCCCeeecccceeeecccccccc
Q psy5674 17 CQNLLMQMLK-DDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHR 61 (145)
Q Consensus 17 ~~~~l~~l~~-~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR 61 (145)
.+..+++.+. .|.|. |..||.....|. ++|..|.+.|-
T Consensus 341 ~~~~~~~~~~~~p~~~-c~~cg~~~~~~~------~~c~~c~~~~~ 379 (389)
T PRK11788 341 LRDLVGEQLKRKPRYR-CRNCGFTARTLY------WHCPSCKAWET 379 (389)
T ss_pred HHHHHHHHHhCCCCEE-CCCCCCCCccce------eECcCCCCccC
Confidence 4556665554 56655 999999999995 79999999884
No 36
>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=70.06 E-value=0.44 Score=27.13 Aligned_cols=29 Identities=28% Similarity=0.543 Sum_probs=16.9
Q ss_pred CccCCCCCCC-Ceeecccceeeeccccccc
Q psy5674 32 YCVDCDAKGP-RWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 32 ~CaDCg~~~p-~w~s~~~GvflC~~Cs~iH 60 (145)
.|.+||.+=| .=.-+.-+..+|..|+..|
T Consensus 5 ~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 5 ICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp B-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 4999998622 1122334788999997654
No 37
>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=70.06 E-value=2.3 Score=28.79 Aligned_cols=31 Identities=19% Similarity=0.748 Sum_probs=25.7
Q ss_pred CCCCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 29 DNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 29 ~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
.|..|.=||.+.. ...||++.|..|++..|-
T Consensus 2 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYAS---GYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 4677999998655 569999999999998865
No 38
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=69.86 E-value=2.1 Score=24.41 Aligned_cols=30 Identities=23% Similarity=0.458 Sum_probs=15.9
Q ss_pred CCccCCCCCCCCeeec---ccceeeecccccccc
Q psy5674 31 KYCVDCDAKGPRWASW---NIGIFLCIRCAGIHR 61 (145)
Q Consensus 31 ~~CaDCg~~~p~w~s~---~~GvflC~~Cs~iHR 61 (145)
+.|..||.+- .+... +.-=++|..|..||-
T Consensus 1 kfC~~CG~~l-~~~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 1 KFCPQCGGPL-ERRIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp -B-TTT--B--EEE--TT-SS-EEEETTTTEEE-
T ss_pred CccccccChh-hhhcCCCCCccceECCCCCCEEe
Confidence 4689999872 23222 455679999999983
No 39
>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=68.58 E-value=2.1 Score=28.94 Aligned_cols=32 Identities=19% Similarity=0.505 Sum_probs=26.0
Q ss_pred CCCCCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 28 DDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 28 p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|..+.|.=||.+.. ...||+..|..|.+..|.
T Consensus 1 ~~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 1 PPQKTCLICGDEAS---GCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCCeecCCcCc---ceEECcchhhhHHHHHHH
Confidence 34567999998665 568999999999998875
No 40
>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=66.56 E-value=3.3 Score=28.73 Aligned_cols=29 Identities=28% Similarity=0.635 Sum_probs=23.6
Q ss_pred CCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 31 KYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 31 ~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
+.|.=||.+.. ...||+..|..|.+..|-
T Consensus 1 ~~C~VCg~~a~---g~hyGv~sC~aC~~FFRR 29 (94)
T cd06966 1 KICGVCGDKAL---GYNFNAITCESCKAFFRR 29 (94)
T ss_pred CCCeeCCCcCc---ceEECcceeeeehheehh
Confidence 35888887655 458999999999998875
No 41
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=66.06 E-value=4.6 Score=28.99 Aligned_cols=23 Identities=39% Similarity=0.804 Sum_probs=20.9
Q ss_pred Ceeecccc--eeeecccccccccCC
Q psy5674 42 RWASWNIG--IFLCIRCAGIHRNLG 64 (145)
Q Consensus 42 ~w~s~~~G--vflC~~Cs~iHR~lg 64 (145)
.|++-.-| |.-|.+|-.+||.-+
T Consensus 52 ewi~~~~G~~VwSC~dC~~iH~ke~ 76 (112)
T COG2158 52 EWISDSNGRKVWSCSDCHWIHRKEG 76 (112)
T ss_pred ceeEcCCCCEEeeccccceecccch
Confidence 89999989 999999999999754
No 42
>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=66.05 E-value=3.7 Score=28.95 Aligned_cols=31 Identities=26% Similarity=0.713 Sum_probs=26.0
Q ss_pred CCCCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 29 DNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 29 ~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
.+..|.=||.+.. ...||+..|..|.+..|.
T Consensus 17 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 47 (101)
T cd07160 17 GNEVCSVCGDKAS---GFHYNVLSCEGCKGFFRR 47 (101)
T ss_pred CCCCCeecCCcCc---ceEECcceehhhhhhhhh
Confidence 4678999998665 468999999999998875
No 43
>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=65.20 E-value=4.2 Score=28.04 Aligned_cols=30 Identities=23% Similarity=0.671 Sum_probs=25.2
Q ss_pred CCCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 30 NKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 30 N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
+..|.=||.+.. ...||+..|..|++..|-
T Consensus 6 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (92)
T cd07163 6 DIPCKVCGDRSS---GKHYGIYACDGCSGFFKR 35 (92)
T ss_pred CCCCcccCCcCc---ccEECceeeeeeeeEEee
Confidence 667999998655 469999999999998875
No 44
>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=63.85 E-value=3.7 Score=28.52 Aligned_cols=31 Identities=26% Similarity=0.608 Sum_probs=25.6
Q ss_pred CCCCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 29 DNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 29 ~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
.+..|.=||.+.. ...||++.|..|.+..|-
T Consensus 4 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKSS---GIHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcCc---ceEECceeehhhHHhhHH
Confidence 4667999998665 458999999999998874
No 45
>KOG3507|consensus
Probab=62.73 E-value=3.8 Score=26.42 Aligned_cols=24 Identities=21% Similarity=0.513 Sum_probs=15.9
Q ss_pred CCccCCCCCCCCeeecccceeeecccc
Q psy5674 31 KYCVDCDAKGPRWASWNIGIFLCIRCA 57 (145)
Q Consensus 31 ~~CaDCg~~~p~w~s~~~GvflC~~Cs 57 (145)
-+|+|||+.+. --.--++-|-+|.
T Consensus 21 YiCgdC~~en~---lk~~D~irCReCG 44 (62)
T KOG3507|consen 21 YICGDCGQENT---LKRGDVIRCRECG 44 (62)
T ss_pred EEecccccccc---ccCCCcEehhhcc
Confidence 36999998764 1234567788883
No 46
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=62.49 E-value=6.8 Score=27.65 Aligned_cols=31 Identities=29% Similarity=0.583 Sum_probs=18.7
Q ss_pred CCCCCCccCCCCCCC-Ceeecccceeeecccc
Q psy5674 27 DDDNKYCVDCDAKGP-RWASWNIGIFLCIRCA 57 (145)
Q Consensus 27 ~p~N~~CaDCg~~~p-~w~s~~~GvflC~~Cs 57 (145)
.+.-.+|.|||.+=| .=.-.--++..|+.|.
T Consensus 77 ~g~yG~C~~Cge~I~~~RL~a~P~a~~Cv~Cq 108 (110)
T TIGR02420 77 DGEYGYCEECGEEIGLRRLEARPTATLCIDCK 108 (110)
T ss_pred CCCCCchhccCCcccHHHHhhCCCccccHHhH
Confidence 356689999999722 1111123456788875
No 47
>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=61.83 E-value=3.9 Score=28.61 Aligned_cols=30 Identities=17% Similarity=0.645 Sum_probs=24.6
Q ss_pred CCCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 30 NKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 30 N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
+..|.=||.+.. ...||+..|..|.+..|-
T Consensus 4 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIAS---GYHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcCc---ceEECceeehhhhHHHHH
Confidence 356999998765 458999999999998874
No 48
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=61.32 E-value=4.3 Score=24.66 Aligned_cols=26 Identities=23% Similarity=0.621 Sum_probs=19.7
Q ss_pred CccCCCCCCCCeeecccceeeeccccc
Q psy5674 32 YCVDCDAKGPRWASWNIGIFLCIRCAG 58 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~GvflC~~Cs~ 58 (145)
.|.=|+.+.+. .-.=+|.|+|.+|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 47788887765 445689999999954
No 49
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=60.52 E-value=6.9 Score=32.52 Aligned_cols=33 Identities=15% Similarity=0.509 Sum_probs=24.1
Q ss_pred CCCCCccCCCCCCCCeeecccceeeecccccccc
Q psy5674 28 DDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHR 61 (145)
Q Consensus 28 p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR 61 (145)
.....|.+||.... =.+..-|-.+|.+|.-+-.
T Consensus 9 ~~~~~Cp~Cg~~~i-v~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 9 EEKLVCPECGSDKL-IYDYERGEIVCADCGLVIE 41 (310)
T ss_pred ccCCcCcCCCCCCe-eEECCCCeEeecccCCccc
Confidence 45678999997432 2245689999999988653
No 50
>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=60.43 E-value=6.2 Score=25.09 Aligned_cols=28 Identities=18% Similarity=0.528 Sum_probs=24.0
Q ss_pred CCCCccCCCCCCCCeeecccceeeeccccc
Q psy5674 29 DNKYCVDCDAKGPRWASWNIGIFLCIRCAG 58 (145)
Q Consensus 29 ~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~ 58 (145)
-.+.|..||..... ..+-.+|.|..|.-
T Consensus 27 TSq~C~~CG~~~~~--~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK--RRSGRVFTCPNCGF 54 (69)
T ss_pred CccCccCccccccc--ccccceEEcCCCCC
Confidence 57899999998777 77888999999955
No 51
>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=58.21 E-value=6.4 Score=26.77 Aligned_cols=28 Identities=18% Similarity=0.600 Sum_probs=23.1
Q ss_pred CccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 32 YCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
.|.=||.+.. ...||+..|..|.+..|-
T Consensus 2 ~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 29 (86)
T cd07157 2 TCQVCGEPAA---GFHHGAYVCEACKKFFMR 29 (86)
T ss_pred CCcccCCcCc---ccEECcceeeEeeeEEec
Confidence 4888887654 469999999999998875
No 52
>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=58.19 E-value=7.5 Score=27.68 Aligned_cols=30 Identities=20% Similarity=0.650 Sum_probs=25.0
Q ss_pred CCCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 30 NKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 30 N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
...|.=||.+.. ...||+..|..|.+..|-
T Consensus 6 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (107)
T cd06955 6 PRICGVCGDRAT---GFHFNAMTCEGCKGFFRR 35 (107)
T ss_pred CCCCeecCCcCc---ccEECcceeeeecceecc
Confidence 466999998665 459999999999998875
No 53
>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=56.43 E-value=5.4 Score=27.48 Aligned_cols=29 Identities=21% Similarity=0.726 Sum_probs=23.5
Q ss_pred CCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 31 KYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 31 ~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
..|.=||.+.. ...||++.|..|.+..|-
T Consensus 2 ~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 30 (91)
T cd07161 2 ELCLVCGDRAS---GYHYNALTCEGCKGFFRR 30 (91)
T ss_pred CCCeeCCCcCc---ceEECceeehhhHHHHHH
Confidence 34888987655 458999999999998874
No 54
>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=56.32 E-value=8.1 Score=26.68 Aligned_cols=32 Identities=22% Similarity=0.639 Sum_probs=25.7
Q ss_pred CCCCCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 28 DDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 28 p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
+....|.=||.+.. ...||+..|..|.+..|.
T Consensus 4 ~p~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (92)
T cd06970 4 NPGLLCRVCGDTSS---GKHYGIYACNGCSGFFKR 35 (92)
T ss_pred CCCCCCeecCCcCc---ccEECccEEeeeeeEeee
Confidence 34557999998765 458999999999998875
No 55
>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=55.62 E-value=5.6 Score=26.54 Aligned_cols=29 Identities=21% Similarity=0.638 Sum_probs=23.7
Q ss_pred CCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 31 KYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 31 ~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
..|.=||.+.. ...||+..|..|.+..|.
T Consensus 3 ~~C~VCg~~a~---g~hyGv~sC~aC~~FFRR 31 (78)
T cd07172 3 KICLVCSDEAS---GCHYGVLTCGSCKVFFKR 31 (78)
T ss_pred CCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 45888997655 469999999999998864
No 56
>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=55.33 E-value=7 Score=26.49 Aligned_cols=28 Identities=29% Similarity=0.763 Sum_probs=23.1
Q ss_pred CccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 32 YCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
.|.=||.+.. ...||+..|..|.+..|-
T Consensus 3 ~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 30 (84)
T cd06962 3 LCVVCGDKAS---GYHYNALTCEGCKGFFRR 30 (84)
T ss_pred CCeecCCcCc---ceEECcceeecceeeeee
Confidence 4888887655 458999999999998875
No 57
>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=53.45 E-value=5.8 Score=27.16 Aligned_cols=30 Identities=27% Similarity=0.697 Sum_probs=24.5
Q ss_pred CCCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 30 NKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 30 N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
+..|.=||.+.. ...||++.|..|.+..|-
T Consensus 3 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (89)
T cd07166 3 VVLCKVCGDKAS---GFHYGVHACEGCKGFFRR 32 (89)
T ss_pred CCCCcccCccCc---ceEEChhhhhhHhhEecc
Confidence 456999998665 458999999999998875
No 58
>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=53.41 E-value=6.7 Score=26.94 Aligned_cols=32 Identities=22% Similarity=0.699 Sum_probs=26.1
Q ss_pred CCCCCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 28 DDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 28 p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
..+..|.=||.+.. ...||+..|..|.+..|-
T Consensus 4 ~~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (90)
T cd07169 4 AEQRTCLICGDRAT---GLHYGIISCEGCKGFFKR 35 (90)
T ss_pred ccCCCCeecCCcCc---ceEECcceehhhHHHHHH
Confidence 35677999998654 468999999999998865
No 59
>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=53.30 E-value=5.3 Score=27.02 Aligned_cols=27 Identities=30% Similarity=0.818 Sum_probs=22.0
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||++.|..|.+..|.
T Consensus 2 C~VCg~~~~---g~hyGv~sC~aCk~FFRR 28 (84)
T cd06965 2 CRVCGDKAS---GFHYGVHACEGCKGFFRR 28 (84)
T ss_pred CcccCccCc---ceEEChhhhhhhhhheee
Confidence 677887654 458999999999999875
No 60
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=53.14 E-value=26 Score=25.05 Aligned_cols=42 Identities=19% Similarity=0.416 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCccCCCCCCCCeeecccc-eeeeccccc
Q psy5674 11 KQIQDKCQNLLMQMLKDDDNKYCVDCDAKGPRWASWNIG-IFLCIRCAG 58 (145)
Q Consensus 11 k~~~e~~~~~l~~l~~~p~N~~CaDCg~~~p~w~s~~~G-vflC~~Cs~ 58 (145)
+++++..+..+..- -.|..|++|++.-.--+-- ...|..|.+
T Consensus 67 ~~i~~~l~~yI~~y------VlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 67 KKLQDLLRRYIKEY------VLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred HHHHHHHHHHHHhc------EECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 34555555455433 4699999999877654433 345888854
No 61
>cd06957 NR_DBD_PNR_like_2 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed of two C4-type zinc fingers. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. 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. Like other members
Probab=52.57 E-value=8.3 Score=25.91 Aligned_cols=27 Identities=22% Similarity=0.625 Sum_probs=20.8
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hyGv~sC~aCk~FFRR 27 (82)
T cd06957 1 CKVCGDKSY---GKHYGVYCCDGCSCFFKR 27 (82)
T ss_pred CCccCccCc---ceEECcceEeeeeeEEEE
Confidence 455776554 458999999999998764
No 62
>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=52.46 E-value=6.3 Score=26.79 Aligned_cols=28 Identities=21% Similarity=0.697 Sum_probs=22.4
Q ss_pred CccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 32 YCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
.|.=||.+.. ...||+..|..|++..|-
T Consensus 1 ~C~VCg~~~~---g~hygv~sC~aC~~FFRR 28 (87)
T cd07162 1 ICRVCGDRAT---GYHFNAMTCEGCKGFFRR 28 (87)
T ss_pred CCcccCCcCc---ceEECcceehhhHHHHHh
Confidence 3777887655 358999999999998865
No 63
>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=52.13 E-value=9.1 Score=26.06 Aligned_cols=29 Identities=28% Similarity=0.686 Sum_probs=23.7
Q ss_pred CCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 31 KYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 31 ~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
..|.=||.+... ..||+..|..|.+..|.
T Consensus 4 ~~C~VCg~~~~g---~hyGv~sC~aC~~FFRR 32 (87)
T cd06967 4 ELCVVCGDKASG---RHYGAVSCEGCKGFFKR 32 (87)
T ss_pred CCCeecCCcCCc---CEeCcceEeeeeeEeee
Confidence 458889986653 58999999999998865
No 64
>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=51.41 E-value=8.9 Score=25.24 Aligned_cols=27 Identities=26% Similarity=0.760 Sum_probs=21.1
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||+..|..|.+..|-
T Consensus 1 C~vCg~~~~---~~hygv~~C~aC~~FFrR 27 (76)
T cd06960 1 CAVCGDRAT---GKHYGVLSCNGCKGFFRR 27 (76)
T ss_pred CCccCccCc---ccEECcceeeeehheeCc
Confidence 555776554 458999999999998875
No 65
>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=51.21 E-value=7 Score=25.94 Aligned_cols=28 Identities=21% Similarity=0.732 Sum_probs=22.9
Q ss_pred CccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 32 YCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
.|.=||.+.. ...||+..|..|.+..|-
T Consensus 2 ~C~VC~~~~~---g~hygv~sC~aC~~FFRR 29 (77)
T cd06956 2 ICAICGDRAS---GKHYGVYSCEGCKGFFKR 29 (77)
T ss_pred CCcccCCcCc---ceEECceeehhHHHHHHH
Confidence 4778887655 469999999999998865
No 66
>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=50.93 E-value=12 Score=20.53 Aligned_cols=30 Identities=20% Similarity=0.382 Sum_probs=13.7
Q ss_pred CCCCccCCCCCCCCeeecccceeeeccccccc
Q psy5674 29 DNKYCVDCDAKGPRWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 29 ~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iH 60 (145)
.++.|.-||++... ...=-..+|..|...|
T Consensus 2 ~~rfC~~CG~~t~~--~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 2 NHRFCGRCGAPTKP--APGGWARRCPSCGHEH 31 (32)
T ss_dssp TTSB-TTT--BEEE---SSSS-EEESSSS-EE
T ss_pred CCcccCcCCccccC--CCCcCEeECCCCcCEe
Confidence 47889999987210 1111235777776544
No 67
>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=50.50 E-value=9.4 Score=26.16 Aligned_cols=31 Identities=29% Similarity=0.722 Sum_probs=25.2
Q ss_pred CCCCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 29 DNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 29 ~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
....|.=||.+.. ...||+..|..|.+..|.
T Consensus 5 ~~~~C~VCg~~~~---g~hyGv~sC~aCk~FFRR 35 (90)
T cd07168 5 SPKLCSICEDKAT---GLHYGIITCEGCKGFFKR 35 (90)
T ss_pred cCCCCcccCCcCc---ceEECceehhhhhHhhhh
Confidence 3456999998655 569999999999998865
No 68
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=49.97 E-value=8.4 Score=20.70 Aligned_cols=28 Identities=21% Similarity=0.372 Sum_probs=17.4
Q ss_pred CCccCCCCCCCCeeecccceeeeccccc
Q psy5674 31 KYCVDCDAKGPRWASWNIGIFLCIRCAG 58 (145)
Q Consensus 31 ~~CaDCg~~~p~w~s~~~GvflC~~Cs~ 58 (145)
..|.-|+..-+.-..-....++|..|..
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCcC
Confidence 3588888886655555778899999864
No 69
>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=49.82 E-value=7.9 Score=25.44 Aligned_cols=27 Identities=19% Similarity=0.639 Sum_probs=20.8
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||++.|..|.+..|.
T Consensus 1 C~VCg~~a~---~~hygv~sC~aCk~FFRR 27 (73)
T cd06963 1 CLICGDEAS---GCHYGVLTCGSCKVFFKR 27 (73)
T ss_pred CcccCccCc---ceEECceeehhhhHhHHH
Confidence 455776544 568999999999998865
No 70
>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=49.57 E-value=8.9 Score=25.05 Aligned_cols=27 Identities=22% Similarity=0.715 Sum_probs=21.0
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||+..|..|.+..|.
T Consensus 1 C~VC~~~~~---g~hygv~sC~aC~~FFRR 27 (72)
T cd07156 1 CGVCGDRAT---GYHFNAMTCEGCKGFFRR 27 (72)
T ss_pred CCccCccCc---ccEECcceehhhhhhhch
Confidence 455776555 358999999999998875
No 71
>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=49.54 E-value=11 Score=25.54 Aligned_cols=29 Identities=31% Similarity=0.770 Sum_probs=24.0
Q ss_pred CCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 31 KYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 31 ~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
..|.=||.+.. ...||+..|..|.+..|-
T Consensus 5 ~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 33 (85)
T cd06964 5 KPCFVCQDKSS---GYHYGVSACEGCKGFFRR 33 (85)
T ss_pred CCCcccCCcCc---ccEECcceeeeeeeEEee
Confidence 46888998655 468999999999998875
No 72
>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=48.96 E-value=10 Score=24.71 Aligned_cols=27 Identities=30% Similarity=0.875 Sum_probs=20.8
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||+..|..|.+..|.
T Consensus 1 C~vC~~~~~---~~hygv~sC~aC~~FFRR 27 (72)
T cd06916 1 CAVCGDKAS---GYHYGVLTCEGCKGFFRR 27 (72)
T ss_pred CCccCccCc---ccEECcceeeeeeeeEeE
Confidence 455776544 468999999999998865
No 73
>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=48.56 E-value=6.8 Score=25.59 Aligned_cols=27 Identities=30% Similarity=0.811 Sum_probs=21.1
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||++.|..|.+..|.
T Consensus 1 C~VCg~~~~---g~hyGv~~C~aC~~FFRR 27 (73)
T cd07158 1 CKVCGDKAS---GFHYGVHSCEGCKGFFRR 27 (73)
T ss_pred CcccCccCc---ceEECcchhhHHHHHHhh
Confidence 455776555 358999999999998875
No 74
>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=48.26 E-value=52 Score=27.54 Aligned_cols=31 Identities=19% Similarity=0.388 Sum_probs=22.6
Q ss_pred CCCCCccCCCCCCCCeeec-------c-cceeeeccccc
Q psy5674 28 DDNKYCVDCDAKGPRWASW-------N-IGIFLCIRCAG 58 (145)
Q Consensus 28 p~N~~CaDCg~~~p~w~s~-------~-~GvflC~~Cs~ 58 (145)
.+...|..||.....|.-+ . --.++|..|..
T Consensus 256 t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~ 294 (299)
T TIGR01385 256 TDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGN 294 (299)
T ss_pred cccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCC
Confidence 5578999999998888733 2 22448999864
No 75
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=48.10 E-value=14 Score=25.56 Aligned_cols=32 Identities=19% Similarity=0.460 Sum_probs=24.7
Q ss_pred CCCCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 29 DNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 29 ~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
.-..|..|+.+.. --+..||..|..|...--.
T Consensus 34 ~~~~Cp~C~~~~V--kR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRTTV--KRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCcce--eeeccCeEEcCCCCCeecc
Confidence 4567999999843 4678999999999765543
No 76
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=47.25 E-value=12 Score=26.06 Aligned_cols=33 Identities=24% Similarity=0.536 Sum_probs=22.3
Q ss_pred cCCCCCCccCCCCCC-------C-Ce---------eecccceeeeccccc
Q psy5674 26 KDDDNKYCVDCDAKG-------P-RW---------ASWNIGIFLCIRCAG 58 (145)
Q Consensus 26 ~~p~N~~CaDCg~~~-------p-~w---------~s~~~GvflC~~Cs~ 58 (145)
+.|+--.|++||.+- | .+ ++=.||-.+|..|..
T Consensus 30 K~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 30 KKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred ccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 346677899999871 1 11 133489999998854
No 77
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=47.12 E-value=9.9 Score=22.77 Aligned_cols=24 Identities=17% Similarity=0.470 Sum_probs=17.3
Q ss_pred CccCCCCCCCCeeecccceeeeccccc
Q psy5674 32 YCVDCDAKGPRWASWNIGIFLCIRCAG 58 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~GvflC~~Cs~ 58 (145)
+|.+||+....- ..+.+-|..|..
T Consensus 4 ~C~~Cg~~~~~~---~~~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIK---SKDVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecC---CCCceECCCCCc
Confidence 699999964422 567788998853
No 78
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=46.97 E-value=24 Score=26.33 Aligned_cols=37 Identities=19% Similarity=0.466 Sum_probs=25.7
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCCCeeecccceeeecccccccccC
Q psy5674 18 QNLLMQMLKDDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRNL 63 (145)
Q Consensus 18 ~~~l~~l~~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~l 63 (145)
+++|..+....+...|.-||- ++-.+|..|.|-|+.+
T Consensus 87 ~~lL~~~~~~~~~~~C~~Cgg---------~rfv~C~~C~Gs~k~~ 123 (147)
T cd03031 87 RKLLKGIRARAGGGVCEGCGG---------ARFVPCSECNGSCKVF 123 (147)
T ss_pred HHHHhhcccccCCCCCCCCCC---------cCeEECCCCCCcceEE
Confidence 445555544456677999985 3446999999999875
No 79
>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=46.12 E-value=8.5 Score=25.21 Aligned_cols=27 Identities=30% Similarity=0.720 Sum_probs=20.9
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hygv~sC~aC~~FFRR 27 (73)
T cd06958 1 CVVCGDKSS---GKHYGQFTCEGCKSFFKR 27 (73)
T ss_pred CCccCccCc---ceEEChhhhhhhhhhhhh
Confidence 455776555 458999999999998865
No 80
>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=46.09 E-value=7 Score=25.77 Aligned_cols=27 Identities=19% Similarity=0.673 Sum_probs=21.0
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VC~~~~~---g~hygv~sC~aCk~FFRR 27 (75)
T cd07155 1 CLVCGDIAS---GYHYGVASCEACKAFFKR 27 (75)
T ss_pred CcccCccCc---ceEEChhhhhhhHHHHHH
Confidence 556776544 468999999999998864
No 81
>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=46.00 E-value=8.6 Score=25.29 Aligned_cols=27 Identities=30% Similarity=0.824 Sum_probs=20.9
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hygv~sC~aC~~FFRR 27 (74)
T cd07179 1 CRVCGGKSS---GFHFGALTCEGCKGFFRR 27 (74)
T ss_pred CcccCccCc---ceEECceeehhHHHHHHH
Confidence 455776554 458999999999998864
No 82
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=45.87 E-value=16 Score=21.60 Aligned_cols=22 Identities=23% Similarity=0.542 Sum_probs=15.0
Q ss_pred CccCCCCCCCCeeecccceeee
Q psy5674 32 YCVDCDAKGPRWASWNIGIFLC 53 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~GvflC 53 (145)
.|.+|+..+.-|+++.-+-..|
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c 22 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGC 22 (50)
T ss_pred CcccCCCcCCeEEecCCCCccc
Confidence 4899998776676665444444
No 83
>cd06969 NR_DBD_NGFI-B DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B. DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B) 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. NGFI-B interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. NGFI-B is a member of the nuclear-steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcrip
Probab=45.44 E-value=12 Score=24.60 Aligned_cols=28 Identities=21% Similarity=0.644 Sum_probs=22.4
Q ss_pred CccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 32 YCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
.|.=||.+.. ...||+..|..|.+..|.
T Consensus 2 ~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 29 (75)
T cd06969 2 LCAVCGDNAA---CQHYGVRTCEGCKGFFKR 29 (75)
T ss_pred CCeecCCcCc---ceEECcceeeeeeeeeee
Confidence 4777887654 458999999999998875
No 84
>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=45.01 E-value=8 Score=25.89 Aligned_cols=27 Identities=30% Similarity=0.791 Sum_probs=21.2
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hyG~~sC~aC~~FFRR 27 (81)
T cd07165 1 CKVCGDKAS---GYHYGVTSCEGCKGFFRR 27 (81)
T ss_pred CCccCccCc---ceEECchhhhhHHHHHHh
Confidence 455776554 459999999999998875
No 85
>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=44.48 E-value=8.6 Score=24.67 Aligned_cols=28 Identities=25% Similarity=0.661 Sum_probs=21.1
Q ss_pred CCccCCCCCCCCeeecccceeeecccccccc
Q psy5674 31 KYCVDCDAKGPRWASWNIGIFLCIRCAGIHR 61 (145)
Q Consensus 31 ~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR 61 (145)
+.|.=||.+.. ..+||++.|..|...-|
T Consensus 1 ~~C~VCg~~~~---~~~ygv~sC~~C~~FFr 28 (70)
T PF00105_consen 1 KKCKVCGDPAS---GYHYGVLSCNACKMFFR 28 (70)
T ss_dssp -BSTTTSSBES---EEETTEEEEHHHHHHHH
T ss_pred CCCeECCCccC---cccccccccccceeeee
Confidence 35888887543 56999999999998543
No 86
>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=44.45 E-value=11 Score=22.25 Aligned_cols=24 Identities=29% Similarity=0.671 Sum_probs=17.1
Q ss_pred CCCccCCCCCCCCeeecccceeeeccc
Q psy5674 30 NKYCVDCDAKGPRWASWNIGIFLCIRC 56 (145)
Q Consensus 30 N~~CaDCg~~~p~w~s~~~GvflC~~C 56 (145)
+..|.+||.+-.+ ..-|..+|..|
T Consensus 17 ~~~Cp~C~~PL~~---~k~g~~~Cv~C 40 (41)
T PF06677_consen 17 DEHCPDCGTPLMR---DKDGKIYCVSC 40 (41)
T ss_pred cCccCCCCCeeEE---ecCCCEECCCC
Confidence 6789999887443 34567778777
No 87
>cd07154 NR_DBD_PNR_like The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. 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. Like other members of the nuclear
Probab=43.29 E-value=14 Score=24.13 Aligned_cols=27 Identities=22% Similarity=0.772 Sum_probs=20.9
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||+..|..|.+..|.
T Consensus 1 C~vCg~~~~---~~hyGv~sC~aC~~FFRR 27 (73)
T cd07154 1 CKVCGDRSS---GKHYGVYACDGCSGFFKR 27 (73)
T ss_pred CcccCccCc---ceEECcceeeeeeeEeee
Confidence 455776544 458999999999998875
No 88
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=42.72 E-value=12 Score=24.13 Aligned_cols=27 Identities=22% Similarity=0.746 Sum_probs=21.4
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.-||.+.. ...||+..|..|.+..|.
T Consensus 2 C~vC~~~~~---~~hygv~~C~aC~~FFRR 28 (70)
T smart00399 2 CCVCGDHAS---GFHFGVCSCRACKAFFRR 28 (70)
T ss_pred CeEeCCcCc---ccEeCCcEechhhhhhhh
Confidence 666777655 348999999999998874
No 89
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=42.67 E-value=16 Score=20.55 Aligned_cols=29 Identities=24% Similarity=0.393 Sum_probs=21.8
Q ss_pred CCCccCCCCCCCCeeecccceeeeccccccc
Q psy5674 30 NKYCVDCDAKGPRWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 30 N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iH 60 (145)
...|-.|+....-+ .+-+..+|..|..++
T Consensus 3 ~~~C~~C~~~~i~~--~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVN--KEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEE--ecCCeEEcccCCcEe
Confidence 45788899877533 678888999997664
No 90
>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=42.59 E-value=16 Score=20.25 Aligned_cols=24 Identities=17% Similarity=0.512 Sum_probs=12.7
Q ss_pred CccCCCCCCCCeeecccceeeeccccc
Q psy5674 32 YCVDCDAKGPRWASWNIGIFLCIRCAG 58 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~GvflC~~Cs~ 58 (145)
.|--|++... | .+-.+|+|..|..
T Consensus 4 ~Cp~C~se~~-y--~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYT-Y--EDGELLVCPECGH 27 (30)
T ss_dssp --TTT------E--E-SSSEEETTTTE
T ss_pred CCCCCCCcce-e--ccCCEEeCCcccc
Confidence 4777887655 3 6778899999964
No 91
>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=42.45 E-value=11 Score=21.08 Aligned_cols=23 Identities=22% Similarity=0.410 Sum_probs=14.3
Q ss_pred CccCCCCCCCCeeecccceeeecccc
Q psy5674 32 YCVDCDAKGPRWASWNIGIFLCIRCA 57 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~GvflC~~Cs 57 (145)
.|++||+... .-.....-|..|.
T Consensus 2 ~C~~Cg~~~~---~~~~~~irC~~CG 24 (32)
T PF03604_consen 2 ICGECGAEVE---LKPGDPIRCPECG 24 (32)
T ss_dssp BESSSSSSE----BSTSSTSSBSSSS
T ss_pred CCCcCCCeeE---cCCCCcEECCcCC
Confidence 5899998754 1233445787774
No 92
>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=42.23 E-value=11 Score=23.46 Aligned_cols=33 Identities=27% Similarity=0.608 Sum_probs=25.7
Q ss_pred CccCCCCC-CCCeeecc-cceeeecccccccccCC
Q psy5674 32 YCVDCDAK-GPRWASWN-IGIFLCIRCAGIHRNLG 64 (145)
Q Consensus 32 ~CaDCg~~-~p~w~s~~-~GvflC~~Cs~iHR~lg 64 (145)
+|..|+.. .|.|=.-. -+..||-.|..-.+..|
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC
Confidence 59999986 57787655 77889999987766655
No 93
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=41.99 E-value=22 Score=20.50 Aligned_cols=29 Identities=24% Similarity=0.482 Sum_probs=19.7
Q ss_pred CccCCCCCCCCeeecccceeeeccccccc
Q psy5674 32 YCVDCDAKGPRWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~GvflC~~Cs~iH 60 (145)
.|..|+..-.....-.+-+..|..|.|+-
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeEE
Confidence 47788886433333457777899998875
No 94
>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=41.75 E-value=11 Score=24.65 Aligned_cols=27 Identities=33% Similarity=0.899 Sum_probs=21.5
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||+..|..|.+..|.
T Consensus 2 C~vCg~~~~---~~hygv~sC~aC~~FFRR 28 (73)
T cd06959 2 CVVCGDKAS---GFHYGVLSCEGCKGFFRR 28 (73)
T ss_pred CceeCCcCc---ceEECceeehhhHHHHHH
Confidence 666776554 458999999999998874
No 95
>KOG3362|consensus
Probab=40.95 E-value=12 Score=28.44 Aligned_cols=34 Identities=26% Similarity=0.624 Sum_probs=27.1
Q ss_pred CCCCCccCCCCCCCCeeecccceeeec-cccccccc
Q psy5674 28 DDNKYCVDCDAKGPRWASWNIGIFLCI-RCAGIHRN 62 (145)
Q Consensus 28 p~N~~CaDCg~~~p~w~s~~~GvflC~-~Cs~iHR~ 62 (145)
|--+.|+-|| -...|.+++-|.-.|. .|-.+|..
T Consensus 116 P~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 116 PLRKFCAVCG-YDSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred CcchhhhhcC-CCchhHHHhcCCceeechhhhhccc
Confidence 5567899999 5666899999998764 68888865
No 96
>PRK00420 hypothetical protein; Validated
Probab=40.93 E-value=53 Score=23.63 Aligned_cols=28 Identities=18% Similarity=0.224 Sum_probs=21.7
Q ss_pred CCCccCCCCCCCCeeecccceeeeccccccc
Q psy5674 30 NKYCVDCDAKGPRWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 30 N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iH 60 (145)
+..|..||++-.. +.-|-..|..|...-
T Consensus 23 ~~~CP~Cg~pLf~---lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCGLPLFE---LKDGEVVCPVHGKVY 50 (112)
T ss_pred cCCCCCCCCccee---cCCCceECCCCCCee
Confidence 4889999987553 377889999997643
No 97
>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=40.79 E-value=9.4 Score=25.86 Aligned_cols=27 Identities=30% Similarity=0.754 Sum_probs=21.6
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||+..|..|.+..|-
T Consensus 2 C~VCg~~~~---g~hygv~sC~aC~~FFRR 28 (85)
T cd06961 2 CVVCGDKAT---GYHYRCITCEGCKGFFRR 28 (85)
T ss_pred CceeCCcCc---ceEEChhhhhhhhHhhHh
Confidence 667887655 458999999999998874
No 98
>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=39.70 E-value=13 Score=24.58 Aligned_cols=27 Identities=22% Similarity=0.628 Sum_probs=20.8
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hyG~~~C~~C~~FFRR 27 (78)
T cd07164 1 CRVCGDRAS---GKHYGVPSCDGCRGFFKR 27 (78)
T ss_pred CcccCccCc---ceEECcchhhhhhhhhhh
Confidence 455776554 358999999999998865
No 99
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.58 E-value=17 Score=29.03 Aligned_cols=25 Identities=28% Similarity=0.569 Sum_probs=21.0
Q ss_pred CCCCCccCCCCCCCCeeecccceeeecccccc
Q psy5674 28 DDNKYCVDCDAKGPRWASWNIGIFLCIRCAGI 59 (145)
Q Consensus 28 p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~i 59 (145)
+-.+.|.-||. +.-+.|.|..|...
T Consensus 307 ~tS~~C~~cg~-------~~~r~~~C~~cg~~ 331 (364)
T COG0675 307 YTSKTCPCCGH-------LSGRLFKCPRCGFV 331 (364)
T ss_pred CCcccccccCC-------ccceeEECCCCCCe
Confidence 45689999999 66899999999774
No 100
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=37.97 E-value=27 Score=20.64 Aligned_cols=32 Identities=19% Similarity=0.334 Sum_probs=19.1
Q ss_pred CCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 31 KYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 31 ~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
+.|.+||..-..=-.-.-..++|..|.-.++.
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeEEC
Confidence 36999998521110001127899999877664
No 101
>KOG4215|consensus
Probab=37.69 E-value=15 Score=31.98 Aligned_cols=32 Identities=25% Similarity=0.610 Sum_probs=26.7
Q ss_pred CCCCCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 28 DDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 28 p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
..+..|+=||.+.+ ---||..-|..|.|.-|.
T Consensus 17 ~~~~~CaICGDkaT---GKHYGA~SCdGCKGFFRR 48 (432)
T KOG4215|consen 17 GVAEFCAICGDKAT---GKHYGAISCDGCKGFFRR 48 (432)
T ss_pred cccchhheeCCccc---ccccceeecCcchHHHHH
Confidence 36889999999876 357999999999997653
No 102
>PHA02942 putative transposase; Provisional
Probab=37.20 E-value=23 Score=30.51 Aligned_cols=28 Identities=21% Similarity=0.358 Sum_probs=21.4
Q ss_pred CCCCccCCCCCCCCeeecccceeeecccccc
Q psy5674 29 DNKYCVDCDAKGPRWASWNIGIFLCIRCAGI 59 (145)
Q Consensus 29 ~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~i 59 (145)
-.+.|..||...+ .++-.+|.|..|.-.
T Consensus 324 TSq~Cs~CG~~~~---~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 324 SSVSCPKCGHKMV---EIAHRYFHCPSCGYE 351 (383)
T ss_pred CCccCCCCCCccC---cCCCCEEECCCCCCE
Confidence 4688999998765 345568999999663
No 103
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=37.10 E-value=24 Score=25.19 Aligned_cols=30 Identities=30% Similarity=0.685 Sum_probs=20.8
Q ss_pred CCCCCCccCCCCCCCCeeecccceeeeccccccc
Q psy5674 27 DDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 27 ~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iH 60 (145)
.|..-.|.+||.. ..+....+.|..|.+..
T Consensus 67 ~p~~~~C~~Cg~~----~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 67 EPVECECEDCSEE----VSPEIDLYRCPKCHGIM 96 (115)
T ss_pred eCcEEEcccCCCE----EecCCcCccCcCCcCCC
Confidence 3788899999953 22222257899998854
No 104
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=36.56 E-value=14 Score=20.77 Aligned_cols=27 Identities=22% Similarity=0.442 Sum_probs=18.4
Q ss_pred CccCCCCCCCCeeecc-cceeeeccccc
Q psy5674 32 YCVDCDAKGPRWASWN-IGIFLCIRCAG 58 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~-~GvflC~~Cs~ 58 (145)
.|.+||..-..+.+.. -....|-.|.+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 5888888655555554 45567888876
No 105
>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=35.78 E-value=13 Score=25.77 Aligned_cols=27 Identities=26% Similarity=0.786 Sum_probs=20.9
Q ss_pred ccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 33 CVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 33 CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
|.=||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VCg~~a~---g~hyGv~sC~aCk~FFRR 27 (93)
T cd07167 1 CPVCGDKVS---GYHYGLLTCESCKGFFKR 27 (93)
T ss_pred CcccCccCc---ceEECchhhhhHHHHHHH
Confidence 555776544 468999999999998864
No 106
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=35.70 E-value=31 Score=23.63 Aligned_cols=31 Identities=16% Similarity=0.458 Sum_probs=23.4
Q ss_pred CCCccCCCCCCCCeeecc--------cceeeeccccccc
Q psy5674 30 NKYCVDCDAKGPRWASWN--------IGIFLCIRCAGIH 60 (145)
Q Consensus 30 N~~CaDCg~~~p~w~s~~--------~GvflC~~Cs~iH 60 (145)
+..|..||.....|..+. --.|+|..|...-
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w 100 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVW 100 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCee
Confidence 789999999988887553 2367999986443
No 107
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=35.11 E-value=12 Score=23.08 Aligned_cols=43 Identities=19% Similarity=0.335 Sum_probs=24.4
Q ss_pred CccCCCCCCCCe--eecccceeeecccccccccCCCccceeeeccc
Q psy5674 32 YCVDCDAKGPRW--ASWNIGIFLCIRCAGIHRNLGVHISRVKSVNL 75 (145)
Q Consensus 32 ~CaDCg~~~p~w--~s~~~GvflC~~Cs~iHR~lg~~is~Vksl~l 75 (145)
.|+=||..-.-. +-+.=| +||.+|..--..+......++++|+
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl~~~~~~~~~~~~~t~ 45 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKLSGFFSDVKIKKNLTL 45 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHhcCcccchhhhhhccH
Confidence 478888873332 345667 7999998543333332333344444
No 108
>PRK04059 rpl34e 50S ribosomal protein L34e; Validated
Probab=33.42 E-value=23 Score=24.50 Aligned_cols=31 Identities=23% Similarity=0.539 Sum_probs=20.0
Q ss_pred CCCCCccCCCCCC-------C----------Ceeecccceeeeccccc
Q psy5674 28 DDNKYCVDCDAKG-------P----------RWASWNIGIFLCIRCAG 58 (145)
Q Consensus 28 p~N~~CaDCg~~~-------p----------~w~s~~~GvflC~~Cs~ 58 (145)
+.--.|+|||.+- | .-++=.||-.+|..|..
T Consensus 32 ~~~pkC~~c~~~L~Gi~~~Rp~~~~rlsK~~K~vsRaYGG~lc~~cvr 79 (88)
T PRK04059 32 PSKAKCAICGKPLNGVPRGRPVEIRKLGKTEKRPERPYGGYLCPKCLK 79 (88)
T ss_pred CCCCcCCCCCCccCCccCcchHHHHhcccccCCcccCcCceecHHHHH
Confidence 3344699999861 1 12344588888888853
No 109
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=33.28 E-value=41 Score=24.77 Aligned_cols=32 Identities=19% Similarity=0.428 Sum_probs=19.3
Q ss_pred CCCCCccCCCCC------------CCCeeecccc-eeeecccccc
Q psy5674 28 DDNKYCVDCDAK------------GPRWASWNIG-IFLCIRCAGI 59 (145)
Q Consensus 28 p~N~~CaDCg~~------------~p~w~s~~~G-vflC~~Cs~i 59 (145)
|-...|..|+.+ -|..+--.+. ...|..|..+
T Consensus 89 ~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 89 PIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKI 133 (147)
T ss_pred CCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCE
Confidence 446899999985 1333333344 3478777554
No 110
>TIGR00598 rad14 DNA repair protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.21 E-value=7.8 Score=30.05 Aligned_cols=28 Identities=14% Similarity=0.316 Sum_probs=21.6
Q ss_pred ccCCCCCCCC-eeecccceeeeccccccc
Q psy5674 33 CVDCDAKGPR-WASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 33 CaDCg~~~p~-w~s~~~GvflC~~Cs~iH 60 (145)
|.+||..... |.--+|++-||..|..-+
T Consensus 1 C~eCg~~~~D~~l~~~F~~~vC~~C~~~~ 29 (172)
T TIGR00598 1 CEECGKIFMDSYLFDHFDCAVCDNCRDKD 29 (172)
T ss_pred CccccchhhhHHHHHHCCChhhhhhhccc
Confidence 8899986333 445679999999998765
No 111
>PF14376 Haem_bd: Haem-binding domain
Probab=32.93 E-value=22 Score=26.06 Aligned_cols=15 Identities=27% Similarity=0.848 Sum_probs=11.7
Q ss_pred CCCccCCCCCCCCee
Q psy5674 30 NKYCVDCDAKGPRWA 44 (145)
Q Consensus 30 N~~CaDCg~~~p~w~ 44 (145)
.+-|.||++.++.|-
T Consensus 41 ~~~CydCHSn~T~~P 55 (137)
T PF14376_consen 41 KNSCYDCHSNNTRYP 55 (137)
T ss_pred HccccccCCCCCCCc
Confidence 356999999977664
No 112
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=32.76 E-value=31 Score=21.13 Aligned_cols=26 Identities=23% Similarity=0.749 Sum_probs=18.7
Q ss_pred CCCCccCCCCCCCCeeecccceeeecccc
Q psy5674 29 DNKYCVDCDAKGPRWASWNIGIFLCIRCA 57 (145)
Q Consensus 29 ~N~~CaDCg~~~p~w~s~~~GvflC~~Cs 57 (145)
-++.|..||+. ......+-+.|..|.
T Consensus 19 ~~~fCP~Cg~~---~m~~~~~r~~C~~Cg 44 (50)
T PRK00432 19 KNKFCPRCGSG---FMAEHLDRWHCGKCG 44 (50)
T ss_pred ccCcCcCCCcc---hheccCCcEECCCcC
Confidence 46689999984 333445888999885
No 113
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=31.79 E-value=22 Score=26.56 Aligned_cols=31 Identities=32% Similarity=0.581 Sum_probs=20.8
Q ss_pred CCCCCccCCCCCC-------C----------Ceeecccceeeeccccc
Q psy5674 28 DDNKYCVDCDAKG-------P----------RWASWNIGIFLCIRCAG 58 (145)
Q Consensus 28 p~N~~CaDCg~~~-------p----------~w~s~~~GvflC~~Cs~ 58 (145)
+.--.|+|||.+- | .-++=.||-.+|..|..
T Consensus 39 ~~~pkC~~cg~~L~GI~~~Rp~e~~rlsK~~KtvsRaYGG~lC~~CVr 86 (135)
T PTZ00074 39 SSGPKCGDCGKVLAGIKALRPTEYKQLSRRERTVSRAYGGVLCHKCVR 86 (135)
T ss_pred CCCCCCCCCCCccCCccCCchHHHHHccccCCCccCCCccchhHHHHH
Confidence 3445699999871 1 12345699999998854
No 114
>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=30.76 E-value=21 Score=21.36 Aligned_cols=27 Identities=19% Similarity=0.445 Sum_probs=19.3
Q ss_pred CccCCCCCCCCeeeccc-ceeeeccccc
Q psy5674 32 YCVDCDAKGPRWASWNI-GIFLCIRCAG 58 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~-GvflC~~Cs~ 58 (145)
.|.+||..--.|.+..- ....|-.|.+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 58899986666765543 4557998876
No 115
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=30.40 E-value=91 Score=23.13 Aligned_cols=42 Identities=17% Similarity=0.446 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCccCCCCCCCCeeecc-cceeeeccccc
Q psy5674 11 KQIQDKCQNLLMQMLKDDDNKYCVDCDAKGPRWASWN-IGIFLCIRCAG 58 (145)
Q Consensus 11 k~~~e~~~~~l~~l~~~p~N~~CaDCg~~~p~w~s~~-~GvflC~~Cs~ 58 (145)
+++++..+..+.. =-.|..|++|++.-.--+ .-...|..|.+
T Consensus 89 ~~i~~~L~~yI~~------yVlC~~C~spdT~l~k~~r~~~l~C~ACGa 131 (138)
T PRK03988 89 RVINEKIDRYVKE------YVICPECGSPDTKLIKEGRIWVLKCEACGA 131 (138)
T ss_pred HHHHHHHHHHHHh------cEECCCCCCCCcEEEEcCCeEEEEcccCCC
Confidence 3444444444443 346999999998776433 33557888854
No 116
>KOG4846|consensus
Probab=30.23 E-value=22 Score=31.52 Aligned_cols=28 Identities=29% Similarity=0.749 Sum_probs=22.5
Q ss_pred CCccCCCCCCCCeeecccceeeecccccccc
Q psy5674 31 KYCVDCDAKGPRWASWNIGIFLCIRCAGIHR 61 (145)
Q Consensus 31 ~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR 61 (145)
--|--||.....+ -|||+-|..|.|.-|
T Consensus 133 ~lCkVCgDkASGf---HYGV~aCEGCKGFFR 160 (538)
T KOG4846|consen 133 SLCKVCGDKASGF---HYGVTACEGCKGFFR 160 (538)
T ss_pred Eeehhhccccccc---eeceeecccchHHHH
Confidence 4588888877644 799999999999654
No 117
>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=29.82 E-value=26 Score=27.44 Aligned_cols=27 Identities=22% Similarity=0.631 Sum_probs=20.4
Q ss_pred CccCCCCCC----CCeeecccceeeeccccc
Q psy5674 32 YCVDCDAKG----PRWASWNIGIFLCIRCAG 58 (145)
Q Consensus 32 ~CaDCg~~~----p~w~s~~~GvflC~~Cs~ 58 (145)
+|.+||.+- ..|-+-+.-...|.+|..
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~ 32 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCGK 32 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccCC
Confidence 699999984 355555677788888876
No 118
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=29.59 E-value=13 Score=28.71 Aligned_cols=31 Identities=16% Similarity=0.411 Sum_probs=20.1
Q ss_pred CCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 31 KYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 31 ~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
-.|..|+..-+.---+++ -|.|..|.+.-..
T Consensus 118 Y~Cp~C~~rytf~eA~~~-~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 118 FFCPNCHIRFTFDEAMEY-GFRCPQCGEMLEE 148 (178)
T ss_pred EECCCCCcEEeHHHHhhc-CCcCCCCCCCCee
Confidence 359999976332222344 5999999886544
No 119
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=29.51 E-value=20 Score=21.25 Aligned_cols=14 Identities=43% Similarity=1.158 Sum_probs=11.3
Q ss_pred eeecccccccccCC
Q psy5674 51 FLCIRCAGIHRNLG 64 (145)
Q Consensus 51 flC~~Cs~iHR~lg 64 (145)
|-|+.|+.+|-.-+
T Consensus 2 yYCi~Cs~~h~e~~ 15 (41)
T PF13119_consen 2 YYCINCSEIHHEKG 15 (41)
T ss_pred EEEEEhHHhHHhhc
Confidence 56999999997644
No 120
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=29.34 E-value=23 Score=24.11 Aligned_cols=31 Identities=23% Similarity=0.442 Sum_probs=22.7
Q ss_pred CccCCCCCCC---Ceeecccc---eeeeccccccccc
Q psy5674 32 YCVDCDAKGP---RWASWNIG---IFLCIRCAGIHRN 62 (145)
Q Consensus 32 ~CaDCg~~~p---~w~s~~~G---vflC~~Cs~iHR~ 62 (145)
.|..||.+-| .+...--| .|-|..|.++...
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~~ 38 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQL 38 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHHH
Confidence 5999999865 33333334 8999999998865
No 121
>KOG4217|consensus
Probab=28.98 E-value=20 Score=32.31 Aligned_cols=30 Identities=20% Similarity=0.568 Sum_probs=25.6
Q ss_pred CCCCCccCCCCCCCCeeecccceeeeccccccc
Q psy5674 28 DDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 28 p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iH 60 (145)
++.+.||-||.... +.-|||--|..|.|.-
T Consensus 267 ~~e~~CAVCgDnAa---CqHYGvRTCEGCKGFF 296 (605)
T KOG4217|consen 267 SAEGLCAVCGDNAA---CQHYGVRTCEGCKGFF 296 (605)
T ss_pred CccceeeecCChHH---hhhcCccccccchHHH
Confidence 56789999998654 8899999999999954
No 122
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=28.74 E-value=14 Score=27.87 Aligned_cols=30 Identities=17% Similarity=0.310 Sum_probs=19.5
Q ss_pred CCccCCCCCCCCeeecccceeeecccccccc
Q psy5674 31 KYCVDCDAKGPRWASWNIGIFLCIRCAGIHR 61 (145)
Q Consensus 31 ~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR 61 (145)
=.|..|+..-+.=-.+++ -|.|..|.+.-.
T Consensus 110 Y~Cp~c~~r~tf~eA~~~-~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 110 FICPNMCVRFTFNEAMEL-NFTCPRCGAMLD 139 (158)
T ss_pred EECCCCCcEeeHHHHHHc-CCcCCCCCCEee
Confidence 359999976332223344 499999988643
No 123
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=28.65 E-value=25 Score=25.09 Aligned_cols=32 Identities=16% Similarity=0.365 Sum_probs=22.6
Q ss_pred CCCCCCccCCCCCCCCeeecccceeeecccccccc
Q psy5674 27 DDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHR 61 (145)
Q Consensus 27 ~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR 61 (145)
.|..-.|.+||...+ ...+..+.|..|.+..-
T Consensus 67 ~p~~~~C~~Cg~~~~---~~~~~~~~CP~Cgs~~~ 98 (114)
T PRK03681 67 QEAECWCETCQQYVT---LLTQRVRRCPQCHGDML 98 (114)
T ss_pred eCcEEEcccCCCeee---cCCccCCcCcCcCCCCc
Confidence 378889999996322 33445578999987653
No 124
>KOG1597|consensus
Probab=28.55 E-value=44 Score=28.20 Aligned_cols=29 Identities=21% Similarity=0.446 Sum_probs=22.8
Q ss_pred CccCCCCCCC-Ceeecccceeeeccccccc
Q psy5674 32 YCVDCDAKGP-RWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 32 ~CaDCg~~~p-~w~s~~~GvflC~~Cs~iH 60 (145)
.|.||....+ .-.+..-|..+|..|.-+-
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl 31 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTVCSECGLVL 31 (308)
T ss_pred CCCCCCCCCCCeeeeccCCceecccCCeee
Confidence 6999998766 4446678999999998753
No 125
>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=28.52 E-value=40 Score=19.64 Aligned_cols=29 Identities=28% Similarity=0.527 Sum_probs=16.4
Q ss_pred CCccCCCCCCC---Ceeecccceeeecccccc
Q psy5674 31 KYCVDCDAKGP---RWASWNIGIFLCIRCAGI 59 (145)
Q Consensus 31 ~~CaDCg~~~p---~w~s~~~GvflC~~Cs~i 59 (145)
++|.=||.+.. .-++-+-++++|..|...
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 46888998743 334445589999999753
No 126
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=28.07 E-value=20 Score=19.15 Aligned_cols=16 Identities=31% Similarity=0.692 Sum_probs=9.2
Q ss_pred cCCCCCCccCCCCCCC
Q psy5674 26 KDDDNKYCVDCDAKGP 41 (145)
Q Consensus 26 ~~p~N~~CaDCg~~~p 41 (145)
+.+.+..|.-|+++.|
T Consensus 14 N~~~~~~C~~C~~~rp 29 (30)
T PF00641_consen 14 NPASRSKCVACGAPRP 29 (30)
T ss_dssp EESSSSB-TTT--BTT
T ss_pred chHHhhhhhCcCCCCc
Confidence 3466778888888766
No 127
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=27.66 E-value=42 Score=27.87 Aligned_cols=28 Identities=18% Similarity=0.527 Sum_probs=18.2
Q ss_pred CccCCCCCCCCeeecccceeeeccccccc
Q psy5674 32 YCVDCDAKGPRWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~GvflC~~Cs~iH 60 (145)
.|.+||..+-.+ +...|-.+|..|.-+-
T Consensus 3 ~CpeCg~~~~~~-d~~~ge~VC~~CG~Vi 30 (285)
T COG1405 3 SCPECGSTNIIT-DYERGEIVCADCGLVL 30 (285)
T ss_pred CCCCCCCcccee-eccCCeEEeccCCEEe
Confidence 588888773322 3347888888887643
No 128
>PF01199 Ribosomal_L34e: Ribosomal protein L34e; InterPro: IPR008195 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 [, ]. A number of eukaryotic and archaebacterial ribosomal proteins belong to the L34e family. These include, vertebrate L34, mosquito L31 [], plant L34 [], yeast putative ribosomal protein YIL052c and archaebacterial L34e.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_i 3IZS_i 4A19_L 4A1D_L 4A18_L 4A1B_L.
Probab=27.33 E-value=18 Score=25.31 Aligned_cols=29 Identities=34% Similarity=0.714 Sum_probs=15.6
Q ss_pred CCCCccCCCCC--C-----C----------Ceeecccceeeecccc
Q psy5674 29 DNKYCVDCDAK--G-----P----------RWASWNIGIFLCIRCA 57 (145)
Q Consensus 29 ~N~~CaDCg~~--~-----p----------~w~s~~~GvflC~~Cs 57 (145)
.--.|+|||.+ + | .=++=.||-.+|..|-
T Consensus 40 ~~pkC~~cg~~L~Gi~~~rp~~~~rl~k~~k~vsRaYGG~lc~~cv 85 (94)
T PF01199_consen 40 KKPKCGDCGKPLNGIPALRPVELRRLSKRQKTVSRAYGGSLCHKCV 85 (94)
T ss_dssp T--BSTSSS-BSSSS-SS-SSTTGTS-CHCH--CCTSSSS-HHHHH
T ss_pred CCCCcCccCCcccccccccHHHHhhcccCCCCCCCCCCccchHHHH
Confidence 33469999985 1 1 1234458888888884
No 129
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=27.23 E-value=16 Score=26.10 Aligned_cols=28 Identities=21% Similarity=0.300 Sum_probs=22.3
Q ss_pred CCCCCCeeecccceeeecccccccccCC
Q psy5674 37 DAKGPRWASWNIGIFLCIRCAGIHRNLG 64 (145)
Q Consensus 37 g~~~p~w~s~~~GvflC~~Cs~iHR~lg 64 (145)
|.++.....+-|.-|.|.-|+..|..++
T Consensus 8 G~~~a~~~v~~f~d~~Cp~C~~~~~~~~ 35 (162)
T PF13462_consen 8 GNPDAPITVTEFFDFQCPHCAKFHEELE 35 (162)
T ss_dssp S-TTTSEEEEEEE-TTSHHHHHHHHHHH
T ss_pred cCCCCCeEEEEEECCCCHhHHHHHHHHh
Confidence 5667778888999999999999998764
No 130
>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
Probab=27.19 E-value=30 Score=30.22 Aligned_cols=30 Identities=20% Similarity=0.607 Sum_probs=20.6
Q ss_pred CCCccCCCCCCCCeeec--ccceeeecccccc
Q psy5674 30 NKYCVDCDAKGPRWASW--NIGIFLCIRCAGI 59 (145)
Q Consensus 30 N~~CaDCg~~~p~w~s~--~~GvflC~~Cs~i 59 (145)
+..|.-||.+...--.+ .-|+++|..|..+
T Consensus 7 ~~~c~fc~~~~~~~~~~~~~~~~~ic~~c~~~ 38 (413)
T TIGR00382 7 TLYCSFCGKSQDEVRKLIAGPGVYICDECIEL 38 (413)
T ss_pred CeecCCCCCChhhcccccCCCCCcCCCchHHH
Confidence 44899999874432222 3458999999763
No 131
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=26.85 E-value=94 Score=21.57 Aligned_cols=32 Identities=19% Similarity=0.542 Sum_probs=24.1
Q ss_pred CCCCCCccCCCCCCCCeeecccceeeeccccccc
Q psy5674 27 DDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 27 ~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iH 60 (145)
+..--.|.-||....... ..||..|..|...-
T Consensus 33 q~a~y~CpfCgk~~vkR~--a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 33 QHAKYFCPFCGKHAVKRQ--AVGIWRCKGCKKTV 64 (90)
T ss_pred HhCCccCCCCCCCceeee--eeEEEEcCCCCCEE
Confidence 356778999998776654 45999999996543
No 132
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=26.55 E-value=99 Score=24.18 Aligned_cols=33 Identities=21% Similarity=0.543 Sum_probs=21.8
Q ss_pred CCCccCCCCCCCCeeecc-cceeeecccccccccC
Q psy5674 30 NKYCVDCDAKGPRWASWN-IGIFLCIRCAGIHRNL 63 (145)
Q Consensus 30 N~~CaDCg~~~p~w~s~~-~GvflC~~Cs~iHR~l 63 (145)
=-.|..|+++++.-.--+ .-.+.|..|.. ||..
T Consensus 98 yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa-~~~v 131 (201)
T PRK12336 98 YVICSECGLPDTRLVKEDRVLMLRCDACGA-HRPV 131 (201)
T ss_pred eEECCCCCCCCcEEEEcCCeEEEEcccCCC-Cccc
Confidence 346999999998776433 22347888844 4443
No 133
>PF04170 NlpE: NlpE N-terminal domain; InterPro: IPR007298 This family represents a bacterial outer membrane lipoprotein that is necessary for signalling by the Cpx pathway []. This pathway responds to cell envelope disturbances and increases the expression of periplasmic protein folding and degradation factors. While the molecular function of the NlpE protein is unknown, it may be involved in detecting bacterial adhesion to abiotic surfaces. NlpE from Escherichia coli and Salmonella typhi is also known to confer copper tolerance in copper-sensitive strains of E. coli, and may be involved in copper efflux and delivery of copper to copper-dependent enzymes [].; PDB: 3LHN_A 2Z4I_B 2Z4H_A.
Probab=26.51 E-value=28 Score=23.43 Aligned_cols=16 Identities=38% Similarity=0.847 Sum_probs=13.4
Q ss_pred cceeeecccccccccC
Q psy5674 48 IGIFLCIRCAGIHRNL 63 (145)
Q Consensus 48 ~GvflC~~Cs~iHR~l 63 (145)
.|++-|-+|.||.-.|
T Consensus 2 ~G~LPCADC~GI~t~L 17 (87)
T PF04170_consen 2 EGTLPCADCPGIKTTL 17 (87)
T ss_dssp EEEEEETTSSEEEEEE
T ss_pred ccEeECCCCCCeEEEE
Confidence 4899999999987654
No 134
>KOG3408|consensus
Probab=25.89 E-value=24 Score=26.02 Aligned_cols=44 Identities=34% Similarity=0.536 Sum_probs=34.8
Q ss_pred ccceeeeccccc---------ccccCCCccceeeecccCCCCHHHHHHHHhhc
Q psy5674 47 NIGIFLCIRCAG---------IHRNLGVHISRVKSVNLDTWTPEQVVSLQQMG 90 (145)
Q Consensus 47 ~~GvflC~~Cs~---------iHR~lg~~is~Vksl~ld~w~~~~i~~l~~~G 90 (145)
-+|-|-|+.|+. .|..--.|-.|||.|.-...|.++-+..--.|
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~~PySQeeAe~A~G~g 106 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELREVPYSQEEAEAAAGMG 106 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhccHHHHHHHhcccCCccHHHHHHhccCC
Confidence 478999999986 66665667789999998888888888775555
No 135
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.79 E-value=27 Score=24.99 Aligned_cols=30 Identities=17% Similarity=0.323 Sum_probs=20.2
Q ss_pred CCCCCccCCCCCCCCeeecccceeeeccccccc
Q psy5674 28 DDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 28 p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iH 60 (145)
|.--.|.+||...+ ...+..+.|..|.+..
T Consensus 69 p~~~~C~~Cg~~~~---~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 69 KVELECKDCSHVFK---PNALDYGVCEKCHSKN 98 (117)
T ss_pred CCEEEhhhCCCccc---cCCccCCcCcCCCCCc
Confidence 66778999995422 2234555699998754
No 136
>PF07762 DUF1618: Protein of unknown function (DUF1618); InterPro: IPR011676 The proteins of this entry are mainly hypothetical proteins expressed by Oryza sativa.
Probab=25.33 E-value=33 Score=24.31 Aligned_cols=15 Identities=27% Similarity=0.607 Sum_probs=13.2
Q ss_pred eeecccceeeecccc
Q psy5674 43 WASWNIGIFLCIRCA 57 (145)
Q Consensus 43 w~s~~~GvflC~~Cs 57 (145)
||++..|+++|.--.
T Consensus 1 WVDl~~GIL~CD~~~ 15 (131)
T PF07762_consen 1 WVDLWRGILFCDVFD 15 (131)
T ss_pred CCcCCCCEEEEECCC
Confidence 889999999998775
No 137
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=24.27 E-value=42 Score=21.62 Aligned_cols=29 Identities=28% Similarity=0.477 Sum_probs=21.2
Q ss_pred cCCCCCCCC-eeecccceeeecccccccccC
Q psy5674 34 VDCDAKGPR-WASWNIGIFLCIRCAGIHRNL 63 (145)
Q Consensus 34 aDCg~~~p~-w~s~~~GvflC~~Cs~iHR~l 63 (145)
.-|+.-.|. +..-+...+.|..| |-||++
T Consensus 23 DGCgEFm~~~g~eg~~~al~CaAC-gCHRnF 52 (60)
T PF04770_consen 23 DGCGEFMPSPGEEGTPEALKCAAC-GCHRNF 52 (60)
T ss_pred ccccccccCCCCCCCcccceeccc-Ccchhc
Confidence 457776666 55556788899888 788876
No 138
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=24.24 E-value=31 Score=21.75 Aligned_cols=29 Identities=17% Similarity=0.494 Sum_probs=22.3
Q ss_pred CCCCCccCCCCCCCCeeecccceeeeccccc
Q psy5674 28 DDNKYCVDCDAKGPRWASWNIGIFLCIRCAG 58 (145)
Q Consensus 28 p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~ 58 (145)
+|.+.|.-||.+.. +--.||.-+|-.|-.
T Consensus 14 kGsr~C~vCg~~~g--liRkygL~~CRqCFR 42 (54)
T PTZ00218 14 KGSRQCRVCSNRHG--LIRKYGLNVCRQCFR 42 (54)
T ss_pred CCCCeeecCCCcch--hhhhcCcchhhHHHH
Confidence 67899999998642 234789999998854
No 139
>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=23.75 E-value=88 Score=19.42 Aligned_cols=40 Identities=20% Similarity=0.377 Sum_probs=23.0
Q ss_pred HHHHHHhcC-C---CC---CCccCCCCCCCCe--eecccceeeeccccc
Q psy5674 19 NLLMQMLKD-D---DN---KYCVDCDAKGPRW--ASWNIGIFLCIRCAG 58 (145)
Q Consensus 19 ~~l~~l~~~-p---~N---~~CaDCg~~~p~w--~s~~~GvflC~~Cs~ 58 (145)
++++-|+.. | .| -+|..|.+.+-.. .....-.|+|..|..
T Consensus 4 ki~d~L~G~d~~~~~~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 4 KILDVLLGDDPTSPSNRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred HHHHHHhCCCCccccCceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 455555543 3 33 4688888764333 233445778888753
No 140
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=23.60 E-value=75 Score=18.32 Aligned_cols=27 Identities=15% Similarity=0.619 Sum_probs=18.5
Q ss_pred CccCCCCCCCCeeecc--------cceeeeccccc
Q psy5674 32 YCVDCDAKGPRWASWN--------IGIFLCIRCAG 58 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~--------~GvflC~~Cs~ 58 (145)
.|..||.....|..+. --.++|.+|..
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~ 36 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGH 36 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCC
Confidence 5888998877776432 23568988863
No 141
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=23.35 E-value=39 Score=17.57 Aligned_cols=11 Identities=45% Similarity=1.147 Sum_probs=6.0
Q ss_pred CCCCCccCCCC
Q psy5674 28 DDNKYCVDCDA 38 (145)
Q Consensus 28 p~N~~CaDCg~ 38 (145)
++.+.|..||+
T Consensus 14 ~~~~fC~~CG~ 24 (26)
T PF13248_consen 14 PDAKFCPNCGA 24 (26)
T ss_pred cccccChhhCC
Confidence 44555666654
No 142
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=23.26 E-value=1.2e+02 Score=23.41 Aligned_cols=34 Identities=12% Similarity=0.401 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHhcCCCCCCccCCCCCCCCeeecccceeeeccccccccc
Q psy5674 12 QIQDKCQNLLMQMLKDDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIHRN 62 (145)
Q Consensus 12 ~~~e~~~~~l~~l~~~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iHR~ 62 (145)
..+..|...++.++..+.+.. +.+|..|.-+|..
T Consensus 113 ~~Ek~H~~~~~~~Le~~~~~~-----------------~~vC~vCGy~~~g 146 (166)
T COG1592 113 KAEKRHAEMFRGLLERLEEGK-----------------VWVCPVCGYTHEG 146 (166)
T ss_pred HHHHHHHHHHHHHHHhhhcCC-----------------EEEcCCCCCcccC
Confidence 356677888888888876554 6677777666654
No 143
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=22.58 E-value=40 Score=21.16 Aligned_cols=23 Identities=26% Similarity=0.621 Sum_probs=15.5
Q ss_pred ccCCCCC-CCCeeecccceeeecc
Q psy5674 33 CVDCDAK-GPRWASWNIGIFLCIR 55 (145)
Q Consensus 33 CaDCg~~-~p~w~s~~~GvflC~~ 55 (145)
|..|+.. ...|+.+.-|-+.|..
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETT
T ss_pred CCCCCCcCCceEEeCCCCcccccC
Confidence 6678866 6678877777777775
No 144
>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=22.35 E-value=60 Score=18.66 Aligned_cols=27 Identities=22% Similarity=0.591 Sum_probs=17.6
Q ss_pred CccCCCCCCCCeeecccc--eeeeccccc
Q psy5674 32 YCVDCDAKGPRWASWNIG--IFLCIRCAG 58 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~G--vflC~~Cs~ 58 (145)
+|..|++---.|+.++.+ .++|.-|..
T Consensus 4 rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp B-TTT--BS-TTSEEETTTTEEEETTT--
T ss_pred ccCCCCCEECCcceEcCCCCEEECcCCCC
Confidence 688999976668888876 899998864
No 145
>PF11261 IRF-2BP1_2: Interferon regulatory factor 2-binding protein zinc finger; InterPro: IPR022750 IRF-2BP1 and IRF-2BP2 are nuclear transcriptional repressor proteins and can inhibit both enhancer-activated and basal transcription. They both contain N-terminal zinc finger and C-terminal RING finger domains []. This entry represents the N-terminal zinc finger domain of IRF-2BP1 and IRF-2BP2.
Probab=22.34 E-value=22 Score=22.30 Aligned_cols=30 Identities=23% Similarity=0.537 Sum_probs=24.8
Q ss_pred CCCccCCCCCCCCeeec-ccceeeecccccc
Q psy5674 30 NKYCVDCDAKGPRWASW-NIGIFLCIRCAGI 59 (145)
Q Consensus 30 N~~CaDCg~~~p~w~s~-~~GvflC~~Cs~i 59 (145)
-..|.=|.-|.+.|+-+ +|+--||-.|...
T Consensus 3 Rq~CyLCdlPr~PWami~df~EpVCRgCvNy 33 (54)
T PF11261_consen 3 RQQCYLCDLPRMPWAMIWDFSEPVCRGCVNY 33 (54)
T ss_pred ceeEEeccCCCCchHHHhhccchhhhhhcCc
Confidence 35699999999999965 7999999999654
No 146
>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]
Probab=22.12 E-value=1.2e+02 Score=20.29 Aligned_cols=26 Identities=23% Similarity=0.473 Sum_probs=21.7
Q ss_pred CCCHHHHHHHHhhccHHHHHHHHhhC
Q psy5674 77 TWTPEQVVSLQQMGNSRARAVYEANI 102 (145)
Q Consensus 77 ~w~~~~i~~l~~~GN~~~n~~~e~~~ 102 (145)
.|+++++.++..+....+-++-.+.+
T Consensus 142 ~~~~~e~~ll~~la~~~a~ai~~~~~ 167 (175)
T COG2203 142 QWSEEELELLEELAEQVAIAIERARL 167 (175)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 69999999999998888887766543
No 147
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=21.88 E-value=44 Score=23.72 Aligned_cols=30 Identities=20% Similarity=0.419 Sum_probs=20.2
Q ss_pred CCCCCCccCCCCCCCCeeecccceeeeccccccc
Q psy5674 27 DDDNKYCVDCDAKGPRWASWNIGIFLCIRCAGIH 60 (145)
Q Consensus 27 ~p~N~~CaDCg~~~p~w~s~~~GvflC~~Cs~iH 60 (145)
.|..-.|-+||... .+....+.|..|.+..
T Consensus 67 vp~~~~C~~Cg~~~----~~~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 67 KPAQAWCWDCSQVV----EIHQHDAQCPHCHGER 96 (113)
T ss_pred eCcEEEcccCCCEE----ecCCcCccCcCCCCCC
Confidence 37888999999532 2223445699998753
No 148
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=21.78 E-value=73 Score=23.49 Aligned_cols=30 Identities=17% Similarity=0.390 Sum_probs=20.7
Q ss_pred CCCccCCCCCCCCeeecccc-eeeecccccc
Q psy5674 30 NKYCVDCDAKGPRWASWNIG-IFLCIRCAGI 59 (145)
Q Consensus 30 N~~CaDCg~~~p~w~s~~~G-vflC~~Cs~i 59 (145)
=-.|..|++|++.-.--+-. .+.|..|...
T Consensus 97 yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 97 YVICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred eEECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 34699999999876643322 3588888543
No 149
>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=20.77 E-value=67 Score=23.40 Aligned_cols=42 Identities=19% Similarity=0.429 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHhcCCCCCCccCCCCCCCCeeecc-cceeeecccccc
Q psy5674 12 QIQDKCQNLLMQMLKDDDNKYCVDCDAKGPRWASWN-IGIFLCIRCAGI 59 (145)
Q Consensus 12 ~~~e~~~~~l~~l~~~p~N~~CaDCg~~~p~w~s~~-~GvflC~~Cs~i 59 (145)
++++..+..+..- -.|..|+++++...--+ .-.+.|..|...
T Consensus 81 ~i~~~L~~fI~~y------VlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 81 QIQDLLDKFIKEY------VLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp HHHHHHHHHHCHH------SSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred HHHHHHHHHHHHE------EEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 3444444444332 35999999998776543 444578888654
No 150
>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=20.73 E-value=37 Score=19.76 Aligned_cols=27 Identities=19% Similarity=0.366 Sum_probs=16.3
Q ss_pred CccCCCCCCCCeeeccc-ceeeeccccc
Q psy5674 32 YCVDCDAKGPRWASWNI-GIFLCIRCAG 58 (145)
Q Consensus 32 ~CaDCg~~~p~w~s~~~-GvflC~~Cs~ 58 (145)
.|.+||..--.+.+++- ....|-.|.+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 47777766544554443 5557777755
No 151
>smart00336 BBOX B-Box-type zinc finger.
Probab=20.47 E-value=91 Score=17.12 Aligned_cols=32 Identities=22% Similarity=0.441 Sum_probs=22.3
Q ss_pred CCCccCCCCCCCCeeecccceeeecccccc-cc
Q psy5674 30 NKYCVDCDAKGPRWASWNIGIFLCIRCAGI-HR 61 (145)
Q Consensus 30 N~~CaDCg~~~p~w~s~~~GvflC~~Cs~i-HR 61 (145)
...|..++.....+.+.+=..++|..|... |+
T Consensus 3 ~~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H~ 35 (42)
T smart00336 3 PPKCDSHGDEPAEFFCEECGALLCRTCDEAEHR 35 (42)
T ss_pred CCcCCCCCCCceEEECCCCCcccccccChhhcC
Confidence 345777775455566777778999999855 54
No 152
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.29 E-value=86 Score=22.93 Aligned_cols=27 Identities=7% Similarity=0.286 Sum_probs=14.6
Q ss_pred ceeeeccccccccc-CCCccceeeeccc
Q psy5674 49 GIFLCIRCAGIHRN-LGVHISRVKSVNL 75 (145)
Q Consensus 49 GvflC~~Cs~iHR~-lg~~is~Vksl~l 75 (145)
..+.|..|.+..-. .+-.--+|+++.+
T Consensus 106 ~~~~CP~Cgs~~~~i~~G~el~i~~ie~ 133 (135)
T PRK03824 106 AFLKCPKCGSRDFEIVKGRGVYIEEIKI 133 (135)
T ss_pred cCcCCcCCCCCCcEEecCceEEEEEEEE
Confidence 44679999875422 2212235666554
No 153
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=20.09 E-value=60 Score=19.71 Aligned_cols=29 Identities=24% Similarity=0.635 Sum_probs=19.6
Q ss_pred CCCccCCCCCCC--Cee-------ecccceeeeccccc
Q psy5674 30 NKYCVDCDAKGP--RWA-------SWNIGIFLCIRCAG 58 (145)
Q Consensus 30 N~~CaDCg~~~p--~w~-------s~~~GvflC~~Cs~ 58 (145)
+..|-=||+..+ .|. +..-.|++|..|..
T Consensus 7 ~~kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 7 ESKCELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHS 44 (47)
T ss_pred CCcccCcCCCCCceEEecCCCCCCCccceeeechHHHH
Confidence 444999998642 222 34668999999864
Done!