Query psy6973
Match_columns 115
No_of_seqs 114 out of 1292
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 23:32:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6973.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6973hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0703|consensus 100.0 9.6E-32 2.1E-36 212.8 4.5 85 15-100 8-92 (287)
2 COG5347 GTPase-activating prot 100.0 2.6E-31 5.6E-36 213.6 5.0 83 17-100 5-87 (319)
3 KOG0706|consensus 100.0 7.3E-31 1.6E-35 216.6 4.6 83 17-100 8-90 (454)
4 PF01412 ArfGap: Putative GTPa 100.0 2.6E-31 5.5E-36 186.0 -0.3 78 21-99 2-79 (116)
5 KOG0704|consensus 100.0 5E-29 1.1E-33 201.2 4.7 80 19-99 6-85 (386)
6 smart00105 ArfGap Putative GTP 99.9 3.1E-29 6.8E-34 174.6 1.8 69 31-99 1-69 (112)
7 PLN03114 ADP-ribosylation fact 99.9 1.2E-27 2.6E-32 194.1 4.5 78 20-98 10-87 (395)
8 PLN03131 hypothetical protein; 99.9 6.5E-25 1.4E-29 187.3 3.9 82 14-99 5-86 (705)
9 PLN03119 putative ADP-ribosyla 99.9 8.7E-25 1.9E-29 185.3 4.0 80 15-98 6-85 (648)
10 KOG0705|consensus 99.9 2.8E-24 6E-29 182.7 1.4 93 6-99 487-579 (749)
11 KOG0521|consensus 99.7 2.2E-19 4.9E-24 158.0 1.3 74 22-96 416-489 (785)
12 KOG1117|consensus 99.6 1.6E-15 3.4E-20 133.8 3.9 82 18-100 284-367 (1186)
13 KOG0818|consensus 99.5 5.9E-16 1.3E-20 130.6 -0.4 69 30-98 5-73 (669)
14 KOG0702|consensus 98.8 2.8E-09 6E-14 90.1 3.7 82 15-98 8-90 (524)
15 KOG0703|consensus 98.7 3E-09 6.4E-14 85.0 1.3 49 52-115 24-73 (287)
16 COG5347 GTPase-activating prot 98.7 4.4E-09 9.4E-14 85.2 1.4 49 52-115 19-68 (319)
17 KOG0704|consensus 98.4 7.7E-08 1.7E-12 78.8 1.3 49 52-115 18-67 (386)
18 smart00105 ArfGap Putative GTP 98.4 7E-08 1.5E-12 67.1 0.8 49 52-115 2-51 (112)
19 KOG0706|consensus 98.4 1.1E-07 2.4E-12 79.7 0.7 48 53-115 23-71 (454)
20 PF01412 ArfGap: Putative GTPa 98.3 8.4E-08 1.8E-12 67.0 -0.6 50 51-115 11-61 (116)
21 PLN03114 ADP-ribosylation fact 98.3 3.4E-07 7.3E-12 75.4 1.5 49 52-115 21-70 (395)
22 KOG0705|consensus 98.1 3.8E-07 8.2E-12 78.9 -1.2 84 17-115 466-561 (749)
23 KOG0521|consensus 97.5 3E-05 6.5E-10 69.4 1.0 49 52-115 425-474 (785)
24 PLN03119 putative ADP-ribosyla 96.6 0.00076 1.6E-08 58.7 1.2 46 52-115 22-68 (648)
25 PLN03131 hypothetical protein; 96.6 0.00082 1.8E-08 59.0 1.0 46 52-115 22-68 (705)
26 KOG1117|consensus 93.0 0.04 8.8E-07 50.4 1.0 50 50-114 295-345 (1186)
27 KOG0818|consensus 88.6 0.088 1.9E-06 45.8 -1.1 48 53-115 8-56 (669)
28 PRK12495 hypothetical protein; 82.4 0.41 8.9E-06 37.4 -0.0 29 30-62 39-67 (226)
29 PF08271 TF_Zn_Ribbon: TFIIB z 81.8 0.53 1.2E-05 27.1 0.3 27 35-62 2-28 (43)
30 PF00643 zf-B_box: B-box zinc 79.3 1.1 2.4E-05 25.1 1.1 34 32-65 2-36 (42)
31 PRK00085 recO DNA repair prote 78.0 1.5 3.3E-05 33.3 1.9 40 23-63 140-180 (247)
32 PF01286 XPA_N: XPA protein N- 77.0 0.68 1.5E-05 26.0 -0.2 28 33-60 3-31 (34)
33 TIGR00613 reco DNA repair prot 75.2 2.2 4.7E-05 32.3 2.0 33 30-62 144-177 (241)
34 smart00401 ZnF_GATA zinc finge 75.1 1.4 2.9E-05 26.6 0.7 36 32-67 2-39 (52)
35 PF00320 GATA: GATA zinc finge 72.2 0.73 1.6E-05 25.7 -0.9 30 36-65 1-32 (36)
36 PF11781 RRN7: RNA polymerase 70.7 2.6 5.7E-05 23.7 1.2 28 32-62 7-34 (36)
37 TIGR02419 C4_traR_proteo phage 67.6 1.9 4E-05 27.1 0.1 33 30-62 28-61 (63)
38 cd07173 NR_DBD_AR DNA-binding 64.7 3 6.5E-05 27.4 0.7 32 31-65 1-32 (82)
39 KOG3362|consensus 64.5 2.1 4.6E-05 31.6 -0.1 34 31-65 116-150 (156)
40 cd07171 NR_DBD_ER DNA-binding 64.4 3.4 7.3E-05 27.2 0.9 31 32-65 2-32 (82)
41 PF10764 Gin: Inhibitor of sig 62.9 4.9 0.00011 23.8 1.3 27 35-62 1-27 (46)
42 cd06966 NR_DBD_CAR DNA-binding 61.1 4.3 9.3E-05 27.3 1.0 29 34-65 1-29 (94)
43 COG1381 RecO Recombinational D 60.7 5.2 0.00011 31.2 1.5 31 30-60 151-182 (251)
44 cd07160 NR_DBD_LXR DNA-binding 60.5 5.7 0.00012 27.2 1.5 31 32-65 17-47 (101)
45 PRK00423 tfb transcription ini 59.5 6.1 0.00013 31.7 1.7 32 31-63 9-40 (310)
46 cd06968 NR_DBD_ROR DNA-binding 58.8 5.3 0.00011 27.0 1.1 32 31-65 3-34 (95)
47 PF14803 Nudix_N_2: Nudix N-te 57.1 2.1 4.6E-05 23.9 -0.9 29 34-63 1-32 (34)
48 cd07170 NR_DBD_ERR DNA-binding 56.5 4.9 0.00011 27.3 0.6 30 33-65 4-33 (97)
49 PF14471 DUF4428: Domain of un 56.4 2.7 5.9E-05 25.4 -0.6 27 35-62 1-29 (51)
50 cd07163 NR_DBD_TLX DNA-binding 56.3 6.5 0.00014 26.3 1.2 31 32-65 5-35 (92)
51 COG1734 DksA DnaK suppressor p 55.6 4.7 0.0001 28.6 0.4 33 31-63 78-111 (120)
52 PRK13715 conjugal transfer pro 55.3 3.3 7.1E-05 26.8 -0.4 30 33-62 34-64 (73)
53 TIGR02420 dksA RNA polymerase- 54.5 5.4 0.00012 27.3 0.6 30 31-60 78-108 (110)
54 PRK11788 tetratricopeptide rep 53.6 15 0.00032 28.8 3.0 38 20-64 342-379 (389)
55 cd06955 NR_DBD_VDR DNA-binding 53.4 8.7 0.00019 26.6 1.5 31 32-65 5-35 (107)
56 cd07166 NR_DBD_REV_ERB DNA-bin 53.2 9 0.00019 25.4 1.5 30 33-65 3-32 (89)
57 KOG3507|consensus 52.6 5.9 0.00013 25.0 0.5 24 34-60 21-44 (62)
58 cd07169 NR_DBD_GCNF_like DNA-b 51.7 7.3 0.00016 26.0 0.9 32 31-65 4-35 (90)
59 cd06965 NR_DBD_Ppar DNA-bindin 51.3 8.5 0.00018 25.3 1.1 27 36-65 2-28 (84)
60 cd06970 NR_DBD_PNR DNA-binding 50.7 9.2 0.0002 25.6 1.2 33 30-65 3-35 (92)
61 cd00202 ZnF_GATA Zinc finger D 50.5 7.2 0.00016 23.7 0.6 33 35-67 1-35 (54)
62 cd07172 NR_DBD_GR_PR DNA-bindi 50.3 7.2 0.00016 25.3 0.6 29 34-65 3-31 (78)
63 PF00105 zf-C4: Zinc finger, C 50.2 7.1 0.00015 24.3 0.6 26 34-62 1-26 (70)
64 TIGR02890 spore_yteA sporulati 49.5 5.7 0.00012 29.3 0.1 41 21-63 76-117 (159)
65 cd07161 NR_DBD_EcR DNA-binding 49.4 7.3 0.00016 26.1 0.6 29 34-65 2-30 (91)
66 PRK11019 hypothetical protein; 49.3 5.2 0.00011 26.9 -0.1 32 32-63 35-67 (88)
67 cd07157 2DBD_NR_DBD1 The first 48.7 9.1 0.0002 25.3 0.9 28 35-65 2-29 (86)
68 cd06962 NR_DBD_FXR DNA-binding 48.6 9.4 0.0002 25.1 1.0 29 34-65 2-30 (84)
69 PF07282 OrfB_Zn_ribbon: Putat 47.6 9 0.0002 23.5 0.8 28 32-61 27-54 (69)
70 PF01258 zf-dskA_traR: Prokary 47.3 1.2 2.5E-05 24.7 -3.1 28 35-62 5-33 (36)
71 cd07168 NR_DBD_DHR4_like DNA-b 46.3 12 0.00026 24.9 1.3 32 31-65 4-35 (90)
72 cd07156 NR_DBD_VDR_like The DN 45.8 11 0.00023 24.0 0.9 27 36-65 1-27 (72)
73 cd07162 NR_DBD_PXR DNA-binding 45.7 8.3 0.00018 25.4 0.4 28 35-65 1-28 (87)
74 PRK10778 dksA RNA polymerase-b 45.3 6.6 0.00014 28.7 -0.2 41 21-63 101-142 (151)
75 COG1997 RPL43A Ribosomal prote 44.7 28 0.0006 23.6 2.8 33 30-64 32-64 (89)
76 cd06958 NR_DBD_COUP_TF DNA-bin 44.6 12 0.00026 23.8 1.0 27 36-65 1-27 (73)
77 PF12760 Zn_Tnp_IS1595: Transp 44.3 22 0.00048 20.4 2.1 38 20-60 7-44 (46)
78 cd07158 NR_DBD_Ppar_like The D 44.0 10 0.00022 24.1 0.6 27 36-65 1-27 (73)
79 cd06964 NR_DBD_RAR DNA-binding 43.8 13 0.00028 24.5 1.1 30 33-65 4-33 (85)
80 cd06967 NR_DBD_TR2_like DNA-bi 43.5 12 0.00026 24.7 0.9 30 33-65 3-32 (87)
81 cd07155 NR_DBD_ER_like DNA-bin 43.2 9.7 0.00021 24.3 0.4 27 36-65 1-27 (75)
82 cd06956 NR_DBD_RXR DNA-binding 42.6 9.1 0.0002 24.6 0.2 28 35-65 2-29 (77)
83 cd06960 NR_DBD_HNF4A DNA-bindi 42.1 13 0.00028 23.7 0.9 27 36-65 1-27 (76)
84 PF04170 NlpE: NlpE N-terminal 40.5 7 0.00015 25.6 -0.6 15 51-65 2-16 (87)
85 COG2174 RPL34A Ribosomal prote 40.2 18 0.00038 24.7 1.3 32 30-61 31-79 (93)
86 COG2158 Uncharacterized protei 40.2 16 0.00035 25.7 1.2 24 45-68 52-77 (112)
87 cd06957 NR_DBD_PNR_like_2 DNA- 40.1 13 0.00028 24.2 0.6 26 36-64 1-26 (82)
88 cd06961 NR_DBD_TR DNA-binding 39.7 13 0.00028 24.4 0.6 27 36-65 2-28 (85)
89 cd06963 NR_DBD_GR_like The DNA 39.2 13 0.00027 23.7 0.5 27 36-65 1-27 (73)
90 cd07179 2DBD_NR_DBD2 The secon 38.9 11 0.00023 24.1 0.1 26 36-64 1-26 (74)
91 cd07165 NR_DBD_DmE78_like DNA- 38.8 12 0.00027 24.2 0.4 27 36-65 1-27 (81)
92 PF04770 ZF-HD_dimer: ZF-HD pr 38.8 13 0.00028 23.5 0.5 31 36-67 21-53 (60)
93 smart00399 ZnF_C4 c4 zinc fing 38.6 14 0.0003 23.1 0.6 27 36-65 2-28 (70)
94 PHA00080 DksA-like zinc finger 38.5 5.5 0.00012 25.6 -1.3 32 31-62 29-61 (72)
95 cd07154 NR_DBD_PNR_like The DN 37.6 16 0.00035 23.1 0.8 27 36-65 1-27 (73)
96 cd07164 NR_DBD_PNR_like_1 DNA- 37.0 18 0.00039 23.2 1.0 27 36-65 1-27 (78)
97 cd06916 NR_DBD_like DNA-bindin 36.9 16 0.00034 23.1 0.7 27 36-65 1-27 (72)
98 PF06827 zf-FPG_IleRS: Zinc fi 36.8 7.9 0.00017 20.3 -0.7 28 34-61 2-29 (30)
99 smart00653 eIF2B_5 domain pres 36.8 34 0.00073 23.7 2.4 43 16-61 66-109 (110)
100 cd06969 NR_DBD_NGFI-B DNA-bind 36.5 18 0.00038 23.1 0.8 28 35-65 2-29 (75)
101 smart00290 ZnF_UBP Ubiquitin C 36.5 25 0.00054 20.1 1.4 22 35-56 1-22 (50)
102 KOG1597|consensus 36.3 21 0.00046 29.2 1.5 28 35-62 2-30 (308)
103 smart00659 RPOLCX RNA polymera 36.2 13 0.00028 21.7 0.2 24 35-61 4-27 (44)
104 PF14376 Haem_bd: Haem-binding 35.9 32 0.0007 24.4 2.2 25 20-49 33-57 (137)
105 cd06959 NR_DBD_EcR_like The DN 35.9 14 0.0003 23.5 0.3 27 36-65 2-28 (73)
106 PRK12336 translation initiatio 35.3 38 0.00083 25.7 2.7 75 16-98 84-167 (201)
107 PF03604 DNA_RNApol_7kD: DNA d 34.2 14 0.0003 20.3 0.1 24 35-61 2-25 (32)
108 PTZ00255 60S ribosomal protein 33.6 51 0.0011 22.3 2.8 39 22-62 25-63 (90)
109 smart00834 CxxC_CXXC_SSSS Puta 31.7 17 0.00038 19.8 0.2 27 35-61 7-34 (41)
110 cd07167 NR_DBD_Lrh-1_like The 30.3 19 0.00041 24.2 0.2 27 36-65 1-27 (93)
111 PTZ00074 60S ribosomal protein 30.3 38 0.00083 24.6 1.8 32 30-61 38-86 (135)
112 PF00641 zf-RanBP: Zn-finger i 30.2 27 0.00058 18.2 0.8 14 31-44 16-29 (30)
113 PF13453 zf-TFIIB: Transcripti 30.0 23 0.00051 19.8 0.6 28 35-62 1-28 (41)
114 COG2124 CypX Cytochrome P450 [ 28.5 17 0.00036 29.8 -0.3 19 89-107 349-367 (411)
115 smart00661 RPOL9 RNA polymeras 27.9 29 0.00063 19.9 0.7 30 34-65 1-32 (52)
116 smart00782 PhnA_Zn_Ribbon PhnA 26.9 37 0.0008 20.2 1.0 29 33-61 7-44 (47)
117 PF01199 Ribosomal_L34e: Ribos 26.6 31 0.00066 23.5 0.8 31 30-60 38-85 (94)
118 PF01780 Ribosomal_L37ae: Ribo 26.6 41 0.00088 22.8 1.3 39 22-62 24-62 (90)
119 COG0675 Transposase and inacti 26.1 31 0.00068 26.3 0.8 25 31-62 307-331 (364)
120 PHA02942 putative transposase; 25.7 31 0.00067 28.6 0.8 28 32-62 324-351 (383)
121 PRK03681 hypA hydrogenase nick 25.3 29 0.00063 24.0 0.4 31 30-63 67-97 (114)
122 PF08792 A2L_zn_ribbon: A2L zi 25.0 34 0.00073 18.8 0.6 29 33-63 3-31 (33)
123 TIGR02605 CxxC_CxxC_SSSS putat 24.8 30 0.00064 20.1 0.4 27 35-61 7-34 (52)
124 PF04161 Arv1: Arv1-like famil 24.5 26 0.00057 26.5 0.1 28 35-62 2-33 (208)
125 PRK10523 lipoprotein involved 24.4 34 0.00074 26.9 0.8 20 45-64 40-59 (234)
126 PF12773 DZR: Double zinc ribb 23.6 45 0.00098 19.0 1.0 29 31-62 10-38 (50)
127 PRK04059 rpl34e 50S ribosomal 23.1 46 0.00099 22.4 1.1 31 30-60 31-78 (88)
128 TIGR01384 TFS_arch transcripti 22.9 45 0.00098 22.1 1.0 29 33-61 62-98 (104)
129 PF13248 zf-ribbon_3: zinc-rib 22.5 43 0.00093 17.0 0.7 10 32-41 15-24 (26)
130 PF06689 zf-C4_ClpX: ClpX C4-t 22.4 51 0.0011 18.7 1.1 28 34-61 2-32 (41)
131 PTZ00218 40S ribosomal protein 22.2 39 0.00083 20.9 0.5 30 30-61 13-42 (54)
132 TIGR00100 hypA hydrogenase nic 22.0 44 0.00096 23.0 0.9 30 30-63 67-96 (115)
133 TIGR00311 aIF-2beta translatio 21.9 87 0.0019 22.4 2.4 43 17-62 84-127 (133)
134 PF13240 zinc_ribbon_2: zinc-r 21.7 65 0.0014 16.1 1.2 11 35-45 1-11 (23)
135 PRK00432 30S ribosomal protein 21.2 49 0.0011 19.7 0.8 26 32-60 19-44 (50)
136 PRK00564 hypA hydrogenase nick 20.9 38 0.00082 23.5 0.3 47 13-62 38-97 (117)
137 PF11261 IRF-2BP1_2: Interfero 20.8 32 0.00069 21.2 -0.0 29 34-62 4-33 (54)
No 1
>KOG0703|consensus
Probab=99.97 E-value=9.6e-32 Score=212.83 Aligned_cols=85 Identities=35% Similarity=0.743 Sum_probs=79.3
Q ss_pred CChHHHHHHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhccccccCCCceeeEEEecCCCcccchhhhhhhhhcc
Q psy6973 15 QSSVETASLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPLNLGLLLCIQCC 94 (115)
Q Consensus 15 ~~~~~~~~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~~~~~~~m~~~gn 94 (115)
..+..+..|.+|++ .|+|++|||||++.|+|||+|+|||||+.|+||||+||+|||+||||+||.|++|+|+.|...||
T Consensus 8 ~~~~~~~~l~~Ll~-~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~GN 86 (287)
T KOG0703|consen 8 SNERNKRRLRELLR-EPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMGN 86 (287)
T ss_pred ccchHHHHHHHHHc-CcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHcc
Confidence 34666888999999 89999999999999999999999999999999999999999999999999999999999999998
Q ss_pred Cccccc
Q psy6973 95 GVHRCL 100 (115)
Q Consensus 95 g~~r~~ 100 (115)
..++.+
T Consensus 87 ~~an~~ 92 (287)
T KOG0703|consen 87 AKANSY 92 (287)
T ss_pred hhhhhh
Confidence 877654
No 2
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=99.97 E-value=2.6e-31 Score=213.60 Aligned_cols=83 Identities=41% Similarity=0.753 Sum_probs=77.9
Q ss_pred hHHHHHHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhccccccCCCceeeEEEecCCCcccchhhhhhhhhccCc
Q psy6973 17 SVETASLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPLNLGLLLCIQCCGV 96 (115)
Q Consensus 17 ~~~~~~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~~~~~~~m~~~gng~ 96 (115)
...+.++..|+. .++|+.|||||+++|+|+|+|||||||++|+||||+||+|||+||||+||.|++++++.|..+||.+
T Consensus 5 ~~~~~~l~~l~~-~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~ 83 (319)
T COG5347 5 SEDRKLLKLLKS-DSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSN 83 (319)
T ss_pred hHHHHHHHHHhh-ccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchh
Confidence 455678888888 9999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred cccc
Q psy6973 97 HRCL 100 (115)
Q Consensus 97 ~r~~ 100 (115)
++-+
T Consensus 84 a~~~ 87 (319)
T COG5347 84 ANRF 87 (319)
T ss_pred hhhH
Confidence 8765
No 3
>KOG0706|consensus
Probab=99.96 E-value=7.3e-31 Score=216.58 Aligned_cols=83 Identities=36% Similarity=0.665 Sum_probs=79.3
Q ss_pred hHHHHHHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhccccccCCCceeeEEEecCCCcccchhhhhhhhhccCc
Q psy6973 17 SVETASLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPLNLGLLLCIQCCGV 96 (115)
Q Consensus 17 ~~~~~~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~~~~~~~m~~~gng~ 96 (115)
++-+.+|++|+. .+.|+.|||||+++|+|+||+||||||++|+++||+||+|||+|||+.||.|+.+|++.|..+||++
T Consensus 8 ~d~~~vfkkLRs-~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~n 86 (454)
T KOG0706|consen 8 QDIQTVFKKLRS-QSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNAN 86 (454)
T ss_pred hhHHHHHHHHhc-CCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchh
Confidence 456789999999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccc
Q psy6973 97 HRCL 100 (115)
Q Consensus 97 ~r~~ 100 (115)
+|-+
T Consensus 87 A~~F 90 (454)
T KOG0706|consen 87 ARVF 90 (454)
T ss_pred HHHH
Confidence 8754
No 4
>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=99.96 E-value=2.6e-31 Score=185.99 Aligned_cols=78 Identities=40% Similarity=0.809 Sum_probs=64.3
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhccccccCCCceeeEEEecCCCcccchhhhhhhhhccCcccc
Q psy6973 21 ASLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPLNLGLLLCIQCCGVHRC 99 (115)
Q Consensus 21 ~~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~~~~~~~m~~~gng~~r~ 99 (115)
++|++|++ .|+|+.|||||+++|+|+|++||+|||..|+++||.||+|+|+||||+||.|++++++.|..+||...+.
T Consensus 2 ~~l~~l~~-~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~~GN~~~n~ 79 (116)
T PF01412_consen 2 KILRELLK-KPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMREGGNKRANS 79 (116)
T ss_dssp HHHHHHHC-STTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHHSHHHHHHH
T ss_pred HHHHHHHc-CcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHHHChHHHHH
Confidence 57899999 9999999999999999999999999999999999999999999999999999999999999998876553
No 5
>KOG0704|consensus
Probab=99.95 E-value=5e-29 Score=201.21 Aligned_cols=80 Identities=29% Similarity=0.589 Sum_probs=72.4
Q ss_pred HHHHHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhccccccCCCceeeEEEecCCCcccchhhhhhhhhccCccc
Q psy6973 19 ETASLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPLNLGLLLCIQCCGVHR 98 (115)
Q Consensus 19 ~~~~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~~~~~~~m~~~gng~~r 98 (115)
+.+.|+.|+- ..+|+.||||++++|+|||++||||||.+|+|+||+||+|||+|||||||.|.+.||+.|.++||.+.+
T Consensus 6 trr~L~~lkp-~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~~ 84 (386)
T KOG0704|consen 6 TRRVLLELKP-QDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERFR 84 (386)
T ss_pred HHHHHHhcCc-cccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhHH
Confidence 3445666655 569999999999999999999999999999999999999999999999999999999999999988766
Q ss_pred c
Q psy6973 99 C 99 (115)
Q Consensus 99 ~ 99 (115)
.
T Consensus 85 e 85 (386)
T KOG0704|consen 85 E 85 (386)
T ss_pred H
Confidence 3
No 6
>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=99.95 E-value=3.1e-29 Score=174.60 Aligned_cols=69 Identities=49% Similarity=0.920 Sum_probs=65.7
Q ss_pred CCCCCccCCCCCCCCeeeeeccchhhhhccccccCCCceeeEEEecCCCcccchhhhhhhhhccCcccc
Q psy6973 31 PGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPLNLGLLLCIQCCGVHRC 99 (115)
Q Consensus 31 ~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~~~~~~~m~~~gng~~r~ 99 (115)
|+|+.||||++++|+|+|++||+|||..|+|+||+||+|||+||||+||.|+++++++|..+||...+.
T Consensus 1 ~~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~w~~~~i~~~~~~GN~~~n~ 69 (112)
T smart00105 1 PGNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTWTEEELRLLQKGGNENANS 69 (112)
T ss_pred CCCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCCCCHHHHHHHHHhhhHHHHH
Confidence 689999999999999999999999999999999999999999999999999999999999999876543
No 7
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.94 E-value=1.2e-27 Score=194.12 Aligned_cols=78 Identities=35% Similarity=0.705 Sum_probs=74.9
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhccccccCCCceeeEEEecCCCcccchhhhhhhhhccCccc
Q psy6973 20 TASLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPLNLGLLLCIQCCGVHR 98 (115)
Q Consensus 20 ~~~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~~~~~~~m~~~gng~~r 98 (115)
.++|++|+. .|+|+.|||||+++|+|+|+|||+|||.+|+|+||+||+|||+|+|++||.|+++++++|..+||..++
T Consensus 10 ~~vfrkL~~-kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~ 87 (395)
T PLN03114 10 ISVFKKLKA-KSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQ 87 (395)
T ss_pred HHHHHHHHh-CcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHH
Confidence 568999999 999999999999999999999999999999999999999999999999999999999999999997654
No 8
>PLN03131 hypothetical protein; Provisional
Probab=99.90 E-value=6.5e-25 Score=187.34 Aligned_cols=82 Identities=21% Similarity=0.419 Sum_probs=76.5
Q ss_pred CCChHHHHHHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhccccccCCCceeeEEEecCCCcccchhhhhhhhhc
Q psy6973 14 LQSSVETASLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPLNLGLLLCIQC 93 (115)
Q Consensus 14 ~~~~~~~~~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~~~~~~~m~~~g 93 (115)
.+.++.+++|++|++ .|+|+.||||++++|+|+|+|||||||+.|+||||+|| ++||||+||.|+.++|++|+.+|
T Consensus 5 kqqErnekiLreLlk-~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLg---hRVKSVTLD~WtdeEV~~Mk~gG 80 (705)
T PLN03131 5 KEEERNEKIIRGLMK-LPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFT---HRVKSVSMSKFTSQDVEALQNGG 80 (705)
T ss_pred HHHHHHHHHHHHHhh-CcCCCccccCCCCCCCeeEeccceEEchhchhhhcccC---cccccccCCCCCHHHHHHHHHhc
Confidence 455777889999999 99999999999999999999999999999999999997 59999999999999999999999
Q ss_pred cCcccc
Q psy6973 94 CGVHRC 99 (115)
Q Consensus 94 ng~~r~ 99 (115)
|..++-
T Consensus 81 N~~AN~ 86 (705)
T PLN03131 81 NQRARE 86 (705)
T ss_pred cHHHHH
Confidence 987653
No 9
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=99.90 E-value=8.7e-25 Score=185.32 Aligned_cols=80 Identities=20% Similarity=0.452 Sum_probs=75.3
Q ss_pred CChHHHHHHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhccccccCCCceeeEEEecCCCcccchhhhhhhhhcc
Q psy6973 15 QSSVETASLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPLNLGLLLCIQCC 94 (115)
Q Consensus 15 ~~~~~~~~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~~~~~~~m~~~gn 94 (115)
+.+..+++|++|++ .|+|+.||||++++|.|+|+|+|+|||+.|+||||+|| ++||||+||.|+.+++++|+.+||
T Consensus 6 ~qERnekILreLlk-lPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDkWT~EEVe~Mk~gGN 81 (648)
T PLN03119 6 EEERNEKIIRGLMK-LPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSKFTSKEVEVLQNGGN 81 (648)
T ss_pred HHHHHHHHHHHHhh-CcCCCccccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCCCCHHHHHHHHHhch
Confidence 44777889999999 99999999999999999999999999999999999998 699999999999999999999999
Q ss_pred Cccc
Q psy6973 95 GVHR 98 (115)
Q Consensus 95 g~~r 98 (115)
..++
T Consensus 82 ~~AN 85 (648)
T PLN03119 82 QRAR 85 (648)
T ss_pred HHHH
Confidence 8765
No 10
>KOG0705|consensus
Probab=99.88 E-value=2.8e-24 Score=182.67 Aligned_cols=93 Identities=48% Similarity=0.915 Sum_probs=89.7
Q ss_pred ccCcCcccCCChHHHHHHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhccccccCCCceeeEEEecCCCcccchh
Q psy6973 6 NKGNGKSRLQSSVETASLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPLNL 85 (115)
Q Consensus 6 ~~~~~~~~~~~~~~~~~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~~~~ 85 (115)
+|+|.|+++.+++++..|+.|+. .+||..|+||+.++|.|||+|+|+.+|+.|+||||+||+|+|+|+||.+|+|+.|+
T Consensus 487 essk~Ks~~~sqsea~a~qairn-~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl 565 (749)
T KOG0705|consen 487 ESSKSKSRLTSQSEAMALQAIRN-MRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVEL 565 (749)
T ss_pred hhhcchhccchhhhHHHHHHHhc-CcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHH
Confidence 67999999999999999999999 99999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhccCcccc
Q psy6973 86 GLLLCIQCCGVHRC 99 (115)
Q Consensus 86 ~~~m~~~gng~~r~ 99 (115)
+..|...||..+..
T Consensus 566 ~~Vm~aiGN~~AN~ 579 (749)
T KOG0705|consen 566 LKVMSAIGNDLANS 579 (749)
T ss_pred HHHHHHhhhhHHHH
Confidence 99999999876654
No 11
>KOG0521|consensus
Probab=99.75 E-value=2.2e-19 Score=158.00 Aligned_cols=74 Identities=53% Similarity=0.985 Sum_probs=70.7
Q ss_pred HHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhccccccCCCceeeEEEecCCCcccchhhhhhhhhccCc
Q psy6973 22 SLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPLNLGLLLCIQCCGV 96 (115)
Q Consensus 22 ~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~~~~~~~m~~~gng~ 96 (115)
.+..++. .|+|..|+|||++.|+|+|+|+||.+|+.|+|+||+||+|+|+|+||+||.|.++++.+|+..||.+
T Consensus 416 ~~~~vq~-~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~ 489 (785)
T KOG0521|consen 416 VIEEVQS-VPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKY 489 (785)
T ss_pred hhhhhhc-CCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcch
Confidence 4788888 9999999999999999999999999999999999999999999999999999999999999998854
No 12
>KOG1117|consensus
Probab=99.56 E-value=1.6e-15 Score=133.84 Aligned_cols=82 Identities=34% Similarity=0.607 Sum_probs=73.3
Q ss_pred HHHHHHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhccccccCCCceeeEEEecCCCc--ccchhhhhhhhhccC
Q psy6973 18 VETASLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDE--WPLNLGLLLCIQCCG 95 (115)
Q Consensus 18 ~~~~~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~--W~~~~~~~m~~~gng 95 (115)
++.+.-.++-. ...|+.|+|||++.|+|||+|+++.||..|+|.||++|..+|+|+|++||. |+.+.++++...||+
T Consensus 284 Sd~evaeriW~-ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~ 362 (1186)
T KOG1117|consen 284 SDYEVAERIWL-NEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNP 362 (1186)
T ss_pred ChHHHHHHHHh-ccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCc
Confidence 34455566666 789999999999999999999999999999999999999999999999996 999999999999987
Q ss_pred ccccc
Q psy6973 96 VHRCL 100 (115)
Q Consensus 96 ~~r~~ 100 (115)
....+
T Consensus 363 ~an~F 367 (1186)
T KOG1117|consen 363 RANRF 367 (1186)
T ss_pred ccccc
Confidence 66543
No 13
>KOG0818|consensus
Probab=99.54 E-value=5.9e-16 Score=130.64 Aligned_cols=69 Identities=39% Similarity=0.780 Sum_probs=62.7
Q ss_pred CCCCCCccCCCCCCCCeeeeeccchhhhhccccccCCCceeeEEEecCCCcccchhhhhhhhhccCccc
Q psy6973 30 VPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPLNLGLLLCIQCCGVHR 98 (115)
Q Consensus 30 ~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~~~~~~~m~~~gng~~r 98 (115)
.+..+.|+|||+++|.|||++-|+|+|.+|+.+||+||.|||.||+|....|.++.++++....+.++.
T Consensus 5 ~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaN 73 (669)
T KOG0818|consen 5 LLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGAN 73 (669)
T ss_pred chhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcc
Confidence 456789999999999999999999999999999999999999999999999999999988876554443
No 14
>KOG0702|consensus
Probab=98.82 E-value=2.8e-09 Score=90.08 Aligned_cols=82 Identities=18% Similarity=0.354 Sum_probs=73.4
Q ss_pred CChHHHHHHHHHHhcCCCCCCccCCCCCCC-CeeeeeccchhhhhccccccCCCceeeEEEecCCCcccchhhhhhhhhc
Q psy6973 15 QSSVETASLQSIRSRVPGNLTCADCAEAGP-TWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPLNLGLLLCIQC 93 (115)
Q Consensus 15 ~~~~~~~~l~~l~~~~~~N~~CaDCg~~~p-~waS~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~~~~~~~m~~~g 93 (115)
++.+.+.+++.|+. +|+|++|++|....+ +|+.+..|-|+|..|+|.-|+| ..-++|||+.|..+++.++.+++.+|
T Consensus 8 ~E~~~ek~iR~l~k-LP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l-~~ahRvksiSmttft~qevs~lQshg 85 (524)
T KOG0702|consen 8 DEYDYEKEIRRLLK-LPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGL-NPAHRVKSISMTTFTDQEVSFLQSHG 85 (524)
T ss_pred chhHHHHHHHHHhc-CCCCCceeeccccccceEEEeeccceeeeccchhhccC-CCccccceeeeeeccccchHHHhhcc
Confidence 44555889999999 999999999999988 9999999999999999999987 44589999999999999999999988
Q ss_pred cCccc
Q psy6973 94 CGVHR 98 (115)
Q Consensus 94 ng~~r 98 (115)
|...+
T Consensus 86 Nq~~k 90 (524)
T KOG0702|consen 86 NQVCK 90 (524)
T ss_pred hhhhh
Confidence 86544
No 15
>KOG0703|consensus
Probab=98.74 E-value=3e-09 Score=84.99 Aligned_cols=49 Identities=41% Similarity=1.049 Sum_probs=44.3
Q ss_pred cchhhhhccccccCCCceeeEEEecCCCccc-chhhhhhhhhccCcccccCccccceEEeeeCCC
Q psy6973 52 GLLLCIQCCGVHRCLGAHVSRVRSLELDEWP-LNLGLLLCIQCCGVHRCLGAHVSRVRFLELDEW 115 (115)
Q Consensus 52 GvflC~~CsgiHR~lG~~is~VkSl~ld~W~-~~~~~~m~~~gng~~r~~g~~is~~~~~~~~~~ 115 (115)
+.-.|.+|..-+ +.|. ..+..++|..|.|+||++|+|||||++++||.|
T Consensus 24 ~N~~CADC~a~~---------------P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W 73 (287)
T KOG0703|consen 24 DNKVCADCGAKG---------------PRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEW 73 (287)
T ss_pred ccCcccccCCCC---------------CCeEEeecCeEEEeecccccccccchhheeeeeecccc
Confidence 356899998863 6688 799999999999999999999999999999999
No 16
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=98.71 E-value=4.4e-09 Score=85.20 Aligned_cols=49 Identities=47% Similarity=1.037 Sum_probs=45.2
Q ss_pred cchhhhhccccccCCCceeeEEEecCCCccc-chhhhhhhhhccCcccccCccccceEEeeeCCC
Q psy6973 52 GLLLCIQCCGVHRCLGAHVSRVRSLELDEWP-LNLGLLLCIQCCGVHRCLGAHVSRVRFLELDEW 115 (115)
Q Consensus 52 GvflC~~CsgiHR~lG~~is~VkSl~ld~W~-~~~~~~m~~~gng~~r~~g~~is~~~~~~~~~~ 115 (115)
+.-.|.+|... .++|. ...+.++|..|.|+||.+|+||++||+|+||.|
T Consensus 19 ~Nk~CaDCga~---------------~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~w 68 (319)
T COG5347 19 SNKKCADCGAP---------------NPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNW 68 (319)
T ss_pred ccCccccCCCC---------------CCceEecccCeEEEeecchhhhccccceeeeeeeecccC
Confidence 56789999876 37799 799999999999999999999999999999999
No 17
>KOG0704|consensus
Probab=98.42 E-value=7.7e-08 Score=78.77 Aligned_cols=49 Identities=35% Similarity=0.895 Sum_probs=43.5
Q ss_pred cchhhhhccccccCCCceeeEEEecCCCccc-chhhhhhhhhccCcccccCccccceEEeeeCCC
Q psy6973 52 GLLLCIQCCGVHRCLGAHVSRVRSLELDEWP-LNLGLLLCIQCCGVHRCLGAHVSRVRFLELDEW 115 (115)
Q Consensus 52 GvflC~~CsgiHR~lG~~is~VkSl~ld~W~-~~~~~~m~~~gng~~r~~g~~is~~~~~~~~~~ 115 (115)
+.-.|.+|... .+.|. .....+||..|+|.||.||+||+.||+||||+|
T Consensus 18 eNk~CfeC~a~---------------NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~w 67 (386)
T KOG0704|consen 18 ENKKCFECGAP---------------NPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKW 67 (386)
T ss_pred cCCceeecCCC---------------CCCeEeecccEEEEEecCCcccccceeeEEEEeeecccc
Confidence 45689999886 36677 688899999999999999999999999999999
No 18
>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=98.41 E-value=7e-08 Score=67.05 Aligned_cols=49 Identities=49% Similarity=1.099 Sum_probs=43.3
Q ss_pred cchhhhhccccccCCCceeeEEEecCCCccc-chhhhhhhhhccCcccccCccccceEEeeeCCC
Q psy6973 52 GLLLCIQCCGVHRCLGAHVSRVRSLELDEWP-LNLGLLLCIQCCGVHRCLGAHVSRVRFLELDEW 115 (115)
Q Consensus 52 GvflC~~CsgiHR~lG~~is~VkSl~ld~W~-~~~~~~m~~~gng~~r~~g~~is~~~~~~~~~~ 115 (115)
|.-+|.+|... .+.|. .+...++|..|.|.||.+|+|||+|++|+||+|
T Consensus 2 ~N~~CaDC~~~---------------~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~w 51 (112)
T smart00105 2 GNKKCFDCGAP---------------NPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTW 51 (112)
T ss_pred CCCcccCCCCC---------------CCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCCC
Confidence 56689999874 25687 688999999999999999999999999999998
No 19
>KOG0706|consensus
Probab=98.35 E-value=1.1e-07 Score=79.67 Aligned_cols=48 Identities=42% Similarity=0.933 Sum_probs=44.5
Q ss_pred chhhhhccccccCCCceeeEEEecCCCccc-chhhhhhhhhccCcccccCccccceEEeeeCCC
Q psy6973 53 LLLCIQCCGVHRCLGAHVSRVRSLELDEWP-LNLGLLLCIQCCGVHRCLGAHVSRVRFLELDEW 115 (115)
Q Consensus 53 vflC~~CsgiHR~lG~~is~VkSl~ld~W~-~~~~~~m~~~gng~~r~~g~~is~~~~~~~~~~ 115 (115)
.-+|.+|++- .++|+ .....+||+.|+++||.||+||++||++.||.|
T Consensus 23 NKvCFDCgAk---------------nPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsW 71 (454)
T KOG0706|consen 23 NKVCFDCGAK---------------NPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSW 71 (454)
T ss_pred CceecccCCC---------------CCCceeecceEEEEEecchhhhccccceEEEeecccccC
Confidence 5689999885 47899 799999999999999999999999999999999
No 20
>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=98.32 E-value=8.4e-08 Score=66.96 Aligned_cols=50 Identities=42% Similarity=1.056 Sum_probs=36.1
Q ss_pred ccchhhhhccccccCCCceeeEEEecCCCccc-chhhhhhhhhccCcccccCccccceEEeeeCCC
Q psy6973 51 LGLLLCIQCCGVHRCLGAHVSRVRSLELDEWP-LNLGLLLCIQCCGVHRCLGAHVSRVRFLELDEW 115 (115)
Q Consensus 51 ~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~-~~~~~~m~~~gng~~r~~g~~is~~~~~~~~~~ 115 (115)
-|.-.|.+|..- .+.|. .....++|..|.|+||.+|+|+++|++|+||.|
T Consensus 11 ~~N~~CaDCg~~---------------~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w 61 (116)
T PF01412_consen 11 PGNKVCADCGAP---------------NPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNW 61 (116)
T ss_dssp TTCTB-TTT-SB---------------S--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS--
T ss_pred cCcCcCCCCCCC---------------CCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCC
Confidence 467799999643 35687 578899999999999999999999999999998
No 21
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=98.25 E-value=3.4e-07 Score=75.39 Aligned_cols=49 Identities=41% Similarity=0.935 Sum_probs=44.4
Q ss_pred cchhhhhccccccCCCceeeEEEecCCCccc-chhhhhhhhhccCcccccCccccceEEeeeCCC
Q psy6973 52 GLLLCIQCCGVHRCLGAHVSRVRSLELDEWP-LNLGLLLCIQCCGVHRCLGAHVSRVRFLELDEW 115 (115)
Q Consensus 52 GvflC~~CsgiHR~lG~~is~VkSl~ld~W~-~~~~~~m~~~gng~~r~~g~~is~~~~~~~~~~ 115 (115)
|.-+|.+|.+. .+.|. .....++|..|.|+||.+|+||++||+++||.|
T Consensus 21 gNk~CaDCga~---------------nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~W 70 (395)
T PLN03114 21 DNKICFDCNAK---------------NPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSW 70 (395)
T ss_pred CCCcCccCCCC---------------CCCceeeccceeehhhhhHhhccCCCCCceeecccCCCC
Confidence 66789999875 36788 789999999999999999999999999999999
No 22
>KOG0705|consensus
Probab=98.10 E-value=3.8e-07 Score=78.94 Aligned_cols=84 Identities=39% Similarity=0.761 Sum_probs=62.6
Q ss_pred hHHHHHHHHHHhcCCCCCCccCCCCCCCCeee-----------eeccchhhhhccccccCCCceeeEEEecCCCccc-ch
Q psy6973 17 SVETASLQSIRSRVPGNLTCADCAEAGPTWAS-----------LNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWP-LN 84 (115)
Q Consensus 17 ~~~~~~l~~l~~~~~~N~~CaDCg~~~p~waS-----------~~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~-~~ 84 (115)
+++++++++|..++.....|.+-......--+ -.-|.-.|.+|... .+.|. .+
T Consensus 466 EERdaWvQai~sqIlaSlq~cessk~Ks~~~sqsea~a~qairn~rgn~~c~dc~~~---------------n~~wAsln 530 (749)
T KOG0705|consen 466 EERDAWVQAIQSQILASLQSCESSKSKSRLTSQSEAMALQAIRNMRGNSHCVDCGTP---------------NPKWASLN 530 (749)
T ss_pred hhHHHHHHHHHHHHHHHHhhhhhhcchhccchhhhHHHHHHHhcCcCCceeeecCCC---------------Cccccccc
Confidence 45678888888877666555332222222222 12378889999765 36788 68
Q ss_pred hhhhhhhhccCcccccCccccceEEeeeCCC
Q psy6973 85 LGLLLCIQCCGVHRCLGAHVSRVRFLELDEW 115 (115)
Q Consensus 85 ~~~~m~~~gng~~r~~g~~is~~~~~~~~~~ 115 (115)
...+||..|+|.||.+|+|+|+||+|.||+|
T Consensus 531 lg~l~cieCsgihr~lgt~lSrvr~LeLDdW 561 (749)
T KOG0705|consen 531 LGVLMCIECSGIHRNLGTHLSRVRSLELDDW 561 (749)
T ss_pred CCeEEEEEchhhhhhhhhhhhhhhccccccC
Confidence 8999999999999999999999999999999
No 23
>KOG0521|consensus
Probab=97.52 E-value=3e-05 Score=69.36 Aligned_cols=49 Identities=53% Similarity=1.106 Sum_probs=43.6
Q ss_pred cchhhhhccccccCCCceeeEEEecCCCccc-chhhhhhhhhccCcccccCccccceEEeeeCCC
Q psy6973 52 GLLLCIQCCGVHRCLGAHVSRVRSLELDEWP-LNLGLLLCIQCCGVHRCLGAHVSRVRFLELDEW 115 (115)
Q Consensus 52 GvflC~~CsgiHR~lG~~is~VkSl~ld~W~-~~~~~~m~~~gng~~r~~g~~is~~~~~~~~~~ 115 (115)
|.-.|.+|... -++|. .+++..+|+.|+|+||.+|.|+|+|++|+||.|
T Consensus 425 gN~~c~Dcg~p---------------~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~ 474 (785)
T KOG0521|consen 425 GNAQCCDCGAP---------------EPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVW 474 (785)
T ss_pred chhhhhhcCCC---------------CCchHhhhhchhhHhhccccccccCchhhhhhhhhhhcc
Confidence 66778888663 47899 799999999999999999999999999999987
No 24
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=96.64 E-value=0.00076 Score=58.71 Aligned_cols=46 Identities=22% Similarity=0.597 Sum_probs=39.4
Q ss_pred cchhhhhccccccCCCceeeEEEecCCCccc-chhhhhhhhhccCcccccCccccceEEeeeCCC
Q psy6973 52 GLLLCIQCCGVHRCLGAHVSRVRSLELDEWP-LNLGLLLCIQCCGVHRCLGAHVSRVRFLELDEW 115 (115)
Q Consensus 52 GvflC~~CsgiHR~lG~~is~VkSl~ld~W~-~~~~~~m~~~gng~~r~~g~~is~~~~~~~~~~ 115 (115)
|.-.|.+|.... ..|. .+...++|..|.|+||.+| .||++|+||+|
T Consensus 22 gNk~CADCgs~~---------------P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDkW 68 (648)
T PLN03119 22 PNRRCINCNSLG---------------PQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSKF 68 (648)
T ss_pred CCCccccCCCCC---------------CCceeeccceEEeccchhhhccCC---ceeeccccCCC
Confidence 566899997642 5677 6888999999999999998 49999999999
No 25
>PLN03131 hypothetical protein; Provisional
Probab=96.56 E-value=0.00082 Score=58.97 Aligned_cols=46 Identities=24% Similarity=0.604 Sum_probs=39.6
Q ss_pred cchhhhhccccccCCCceeeEEEecCCCccc-chhhhhhhhhccCcccccCccccceEEeeeCCC
Q psy6973 52 GLLLCIQCCGVHRCLGAHVSRVRSLELDEWP-LNLGLLLCIQCCGVHRCLGAHVSRVRFLELDEW 115 (115)
Q Consensus 52 GvflC~~CsgiHR~lG~~is~VkSl~ld~W~-~~~~~~m~~~gng~~r~~g~~is~~~~~~~~~~ 115 (115)
|.-.|.+|... ...|. .....++|..|.|+||.+| .+|++|+||+|
T Consensus 22 gNk~CADCga~---------------~P~WASiNlGIFICi~CSGIHRsLg---hRVKSVTLD~W 68 (705)
T PLN03131 22 PNRRCINCNSL---------------GPQFVCTNFWTFICMTCSGIHREFT---HRVKSVSMSKF 68 (705)
T ss_pred CCCccccCCCC---------------CCCeeEeccceEEchhchhhhcccC---cccccccCCCC
Confidence 56789999764 25677 6888999999999999997 39999999999
No 26
>KOG1117|consensus
Probab=93.00 E-value=0.04 Score=50.42 Aligned_cols=50 Identities=36% Similarity=0.726 Sum_probs=41.8
Q ss_pred eccchhhhhccccccCCCceeeEEEecCCCccc-chhhhhhhhhccCcccccCccccceEEeeeCC
Q psy6973 50 NLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWP-LNLGLLLCIQCCGVHRCLGAHVSRVRFLELDE 114 (115)
Q Consensus 50 ~~GvflC~~CsgiHR~lG~~is~VkSl~ld~W~-~~~~~~m~~~gng~~r~~g~~is~~~~~~~~~ 114 (115)
|-..--|.+|++- -++|. .++-..+|+.|.|-||++|.-+|+|++++||.
T Consensus 295 ne~nr~cadC~ss---------------rPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~ 345 (1186)
T KOG1117|consen 295 NEENRECADCGSS---------------RPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDP 345 (1186)
T ss_pred ccccccccccCCC---------------CCcccccccceEEcccCCCccccCCCccccccccccCc
Confidence 3344568888763 46799 78889999999999999999999999999984
No 27
>KOG0818|consensus
Probab=88.58 E-value=0.088 Score=45.81 Aligned_cols=48 Identities=44% Similarity=0.996 Sum_probs=41.4
Q ss_pred chhhhhccccccCCCceeeEEEecCCCccc-chhhhhhhhhccCcccccCccccceEEeeeCCC
Q psy6973 53 LLLCIQCCGVHRCLGAHVSRVRSLELDEWP-LNLGLLLCIQCCGVHRCLGAHVSRVRFLELDEW 115 (115)
Q Consensus 53 vflC~~CsgiHR~lG~~is~VkSl~ld~W~-~~~~~~m~~~gng~~r~~g~~is~~~~~~~~~~ 115 (115)
.-+|.+|++- ...|. ..-..++|..|--+||++|-|||-||.|.-.-|
T Consensus 8 ~evC~DC~~~---------------dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W 56 (669)
T KOG0818|consen 8 SEVCADCSGP---------------DPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPW 56 (669)
T ss_pred hhhhcccCCC---------------CCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCC
Confidence 4589999885 35688 688889999999999999999999999987766
No 28
>PRK12495 hypothetical protein; Provisional
Probab=82.35 E-value=0.41 Score=37.44 Aligned_cols=29 Identities=21% Similarity=0.390 Sum_probs=24.4
Q ss_pred CCCCCCccCCCCCCCCeeeeeccchhhhhcccc
Q psy6973 30 VPGNLTCADCAEAGPTWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 30 ~~~N~~CaDCg~~~p~waS~~~GvflC~~Csgi 62 (115)
...+..|-+||.|-|.. -|+..|..|..+
T Consensus 39 tmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~ 67 (226)
T PRK12495 39 TMTNAHCDECGDPIFRH----DGQEFCPTCQQP 67 (226)
T ss_pred ccchhhcccccCcccCC----CCeeECCCCCCc
Confidence 35799999999999932 699999999865
No 29
>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=81.78 E-value=0.53 Score=27.05 Aligned_cols=27 Identities=26% Similarity=0.546 Sum_probs=20.2
Q ss_pred CccCCCCCCCCeeeeeccchhhhhcccc
Q psy6973 35 TCADCAEAGPTWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 35 ~CaDCg~~~p~waS~~~GvflC~~Csgi 62 (115)
.|..||+.. .-.....|-++|..|+.+
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCE
Confidence 588999976 334456899999999765
No 30
>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=79.33 E-value=1.1 Score=25.07 Aligned_cols=34 Identities=18% Similarity=0.310 Sum_probs=27.4
Q ss_pred CCCCccCCCCCCCCeeeeeccchhhhhcccc-ccC
Q psy6973 32 GNLTCADCAEAGPTWASLNLGLLLCIQCCGV-HRC 65 (115)
Q Consensus 32 ~N~~CaDCg~~~p~waS~~~GvflC~~Csgi-HR~ 65 (115)
.+..|..+......+-..+-..++|..|... |+.
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 3577888888777788888899999999987 876
No 31
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=77.96 E-value=1.5 Score=33.26 Aligned_cols=40 Identities=23% Similarity=0.331 Sum_probs=30.0
Q ss_pred HHHHHhcCCCCCCccCCCCCCC-Ceeeeeccchhhhhccccc
Q psy6973 23 LQSIRSRVPGNLTCADCAEAGP-TWASLNLGLLLCIQCCGVH 63 (115)
Q Consensus 23 l~~l~~~~~~N~~CaDCg~~~p-~waS~~~GvflC~~CsgiH 63 (115)
|+.+.= .|.-..|+.||.+.. .+.+...|.++|..|...|
T Consensus 140 L~~~G~-~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~~~ 180 (247)
T PRK00085 140 LAELGY-GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGDPY 180 (247)
T ss_pred HHHcCC-ccchhhHhcCCCCCCceEEecccCCcccccccCcc
Confidence 333333 556679999998865 7888999999999997433
No 32
>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=76.98 E-value=0.68 Score=26.05 Aligned_cols=28 Identities=21% Similarity=0.558 Sum_probs=16.4
Q ss_pred CCCccCCCCC-CCCeeeeeccchhhhhcc
Q psy6973 33 NLTCADCAEA-GPTWASLNLGLLLCIQCC 60 (115)
Q Consensus 33 N~~CaDCg~~-~p~waS~~~GvflC~~Cs 60 (115)
-..|.+|+.+ .-.|..-+|+.-+|..|.
T Consensus 3 ~~~C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 3 YPKCDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp -EE-TTT--EES-SSCCCCTS-S--TTT-
T ss_pred CchHhHhCCHHHHHHHHHhCCcccccccc
Confidence 4579999997 457889999999999984
No 33
>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=75.20 E-value=2.2 Score=32.27 Aligned_cols=33 Identities=27% Similarity=0.433 Sum_probs=27.0
Q ss_pred CCCCCCccCCCCCCC-Ceeeeeccchhhhhcccc
Q psy6973 30 VPGNLTCADCAEAGP-TWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 30 ~~~N~~CaDCg~~~p-~waS~~~GvflC~~Csgi 62 (115)
.|.-..|+.||..++ .+.|...|.++|.+|...
T Consensus 144 ~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 144 ALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred CcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 566679999998654 677889999999999864
No 34
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=75.10 E-value=1.4 Score=26.63 Aligned_cols=36 Identities=25% Similarity=0.554 Sum_probs=28.5
Q ss_pred CCCCccCCCCC-CCCeeeeeccc-hhhhhccccccCCC
Q psy6973 32 GNLTCADCAEA-GPTWASLNLGL-LLCIQCCGVHRCLG 67 (115)
Q Consensus 32 ~N~~CaDCg~~-~p~waS~~~Gv-flC~~CsgiHR~lG 67 (115)
....|..|+.. .|.|-....|. +||-.|.-..+..+
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~ 39 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHG 39 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcC
Confidence 46789999986 58898888886 99999987655444
No 35
>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=72.17 E-value=0.73 Score=25.74 Aligned_cols=30 Identities=27% Similarity=0.606 Sum_probs=21.0
Q ss_pred ccCCCCC-CCCeeeeeccch-hhhhccccccC
Q psy6973 36 CADCAEA-GPTWASLNLGLL-LCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~-~p~waS~~~Gvf-lC~~CsgiHR~ 65 (115)
|..|+.. .|.|-....|.. ||-.|.-.++.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk 32 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKK 32 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHH
Confidence 7889987 689998888877 99999765543
No 36
>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=70.69 E-value=2.6 Score=23.70 Aligned_cols=28 Identities=25% Similarity=0.602 Sum_probs=22.9
Q ss_pred CCCCccCCCCCCCCeeeeeccchhhhhcccc
Q psy6973 32 GNLTCADCAEAGPTWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 32 ~N~~CaDCg~~~p~waS~~~GvflC~~Csgi 62 (115)
.+..|..|++. |....-|-+.|..|..+
T Consensus 7 ~~~~C~~C~~~---~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 7 PNEPCPVCGSR---WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCCcCCCCCCe---EeEccCCEEEhhhCceE
Confidence 45679999988 77889999999999653
No 37
>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=67.56 E-value=1.9 Score=27.10 Aligned_cols=33 Identities=27% Similarity=0.557 Sum_probs=23.2
Q ss_pred CCCCCCccCCCCCCCCee-eeeccchhhhhcccc
Q psy6973 30 VPGNLTCADCAEAGPTWA-SLNLGLLLCIQCCGV 62 (115)
Q Consensus 30 ~~~N~~CaDCg~~~p~wa-S~~~GvflC~~Csgi 62 (115)
.++..+|.|||.+=|.=- -..-|+..|..|...
T Consensus 28 ~~s~g~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~ 61 (63)
T TIGR02419 28 GPSLRECEDCGEPIPEARREALPGVTRCVSCQEI 61 (63)
T ss_pred CCCCCeeccCCCcChHHHHhhcCCcCCcHHHHhh
Confidence 456789999999866321 234478889999764
No 38
>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=64.65 E-value=3 Score=27.41 Aligned_cols=32 Identities=25% Similarity=0.527 Sum_probs=25.6
Q ss_pred CCCCCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 31 PGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 31 ~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|..+.|.-||.+.. ...||+..|..|.+..|-
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 34567999997665 468999999999998763
No 39
>KOG3362|consensus
Probab=64.51 E-value=2.1 Score=31.62 Aligned_cols=34 Identities=26% Similarity=0.555 Sum_probs=26.0
Q ss_pred CCCCCccCCCCCCCCeeeeeccchhhh-hccccccC
Q psy6973 31 PGNLTCADCAEAGPTWASLNLGLLLCI-QCCGVHRC 65 (115)
Q Consensus 31 ~~N~~CaDCg~~~p~waS~~~GvflC~-~CsgiHR~ 65 (115)
|.-+.|+-|| ....|..++.|.-.|. .|-.+|..
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 3446899999 6666888899988886 77777754
No 40
>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=64.36 E-value=3.4 Score=27.15 Aligned_cols=31 Identities=19% Similarity=0.498 Sum_probs=25.5
Q ss_pred CCCCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 32 GNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 32 ~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
.|..|.-||.+.. ...||+..|..|.+..|-
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 4678999997664 469999999999998764
No 41
>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=62.87 E-value=4.9 Score=23.82 Aligned_cols=27 Identities=19% Similarity=0.469 Sum_probs=20.8
Q ss_pred CccCCCCCCCCeeeeeccchhhhhcccc
Q psy6973 35 TCADCAEAGPTWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 35 ~CaDCg~~~p~waS~~~GvflC~~Csgi 62 (115)
.|.=|+.+.++ --.=+|.|+|.+|-.-
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~~ 27 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEKE 27 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHHH
Confidence 47889988887 3456799999999663
No 42
>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=61.10 E-value=4.3 Score=27.31 Aligned_cols=29 Identities=21% Similarity=0.535 Sum_probs=23.3
Q ss_pred CCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 34 LTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 34 ~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
+.|.-||.+.. ...||+..|..|.+..|-
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 45888987655 459999999999998764
No 43
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=60.75 E-value=5.2 Score=31.16 Aligned_cols=31 Identities=29% Similarity=0.597 Sum_probs=26.6
Q ss_pred CCCCCCccCCCCCCC-Ceeeeeccchhhhhcc
Q psy6973 30 VPGNLTCADCAEAGP-TWASLNLGLLLCIQCC 60 (115)
Q Consensus 30 ~~~N~~CaDCg~~~p-~waS~~~GvflC~~Cs 60 (115)
.|.=..|+.||.+.+ ...|.-.|-++|..|+
T Consensus 151 ~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 151 GPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred ccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 455678999999965 6889999999999998
No 44
>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=60.50 E-value=5.7 Score=27.18 Aligned_cols=31 Identities=29% Similarity=0.708 Sum_probs=25.5
Q ss_pred CCCCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 32 GNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 32 ~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
.+..|.-||.+.. ...||+..|..|.+..|-
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 4667999998665 469999999999998764
No 45
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=59.47 E-value=6.1 Score=31.68 Aligned_cols=32 Identities=22% Similarity=0.501 Sum_probs=23.5
Q ss_pred CCCCCccCCCCCCCCeeeeeccchhhhhccccc
Q psy6973 31 PGNLTCADCAEAGPTWASLNLGLLLCIQCCGVH 63 (115)
Q Consensus 31 ~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiH 63 (115)
.....|.+||.+.. =.....|-.+|.+|+-|-
T Consensus 9 ~~~~~Cp~Cg~~~i-v~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 9 EEKLVCPECGSDKL-IYDYERGEIVCADCGLVI 40 (310)
T ss_pred ccCCcCcCCCCCCe-eEECCCCeEeecccCCcc
Confidence 45678999997433 223577999999999864
No 46
>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=58.80 E-value=5.3 Score=26.96 Aligned_cols=32 Identities=22% Similarity=0.621 Sum_probs=25.9
Q ss_pred CCCCCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 31 PGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 31 ~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
-.+..|.-||.+.. ...||+..|..|.+..|-
T Consensus 3 ~~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 3 IEVIPCKICGDKSS---GIHYGVITCEGCKGFFRR 34 (95)
T ss_pred ccccCCcccCCcCc---ceEECceeehhhHHhhHH
Confidence 35678999998765 458999999999998763
No 47
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=57.13 E-value=2.1 Score=23.88 Aligned_cols=29 Identities=21% Similarity=0.373 Sum_probs=13.9
Q ss_pred CCccCCCCCCCCeee---eeccchhhhhccccc
Q psy6973 34 LTCADCAEAGPTWAS---LNLGLLLCIQCCGVH 63 (115)
Q Consensus 34 ~~CaDCg~~~p~waS---~~~GvflC~~CsgiH 63 (115)
++|..||.+- ++.. =+.-=.+|..|..||
T Consensus 1 kfC~~CG~~l-~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 1 KFCPQCGGPL-ERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp -B-TTT--B--EEE--TT-SS-EEEETTTTEEE
T ss_pred CccccccChh-hhhcCCCCCccceECCCCCCEE
Confidence 4788888772 1211 133356888888877
No 48
>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=56.46 E-value=4.9 Score=27.26 Aligned_cols=30 Identities=17% Similarity=0.495 Sum_probs=24.4
Q ss_pred CCCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 33 NLTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 33 N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
+..|.-||.+.. ...||+..|..|.+..|-
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 357999998765 458999999999998763
No 49
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=56.40 E-value=2.7 Score=25.35 Aligned_cols=27 Identities=22% Similarity=0.557 Sum_probs=19.2
Q ss_pred CccCCCCCCCCeee--eeccchhhhhcccc
Q psy6973 35 TCADCAEAGPTWAS--LNLGLLLCIQCCGV 62 (115)
Q Consensus 35 ~CaDCg~~~p~waS--~~~GvflC~~Csgi 62 (115)
.|+=||.+-.-... +.=| +||.+|..-
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~K 29 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKK 29 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHH
Confidence 47888887665543 4557 899999864
No 50
>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=56.31 E-value=6.5 Score=26.28 Aligned_cols=31 Identities=19% Similarity=0.596 Sum_probs=25.4
Q ss_pred CCCCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 32 GNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 32 ~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
-+..|.-||.+... ..||+..|..|.+..|-
T Consensus 5 ~~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 35 (92)
T cd07163 5 LDIPCKVCGDRSSG---KHYGIYACDGCSGFFKR 35 (92)
T ss_pred cCCCCcccCCcCcc---cEECceeeeeeeeEEee
Confidence 47789999986554 59999999999998764
No 51
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=55.62 E-value=4.7 Score=28.58 Aligned_cols=33 Identities=24% Similarity=0.416 Sum_probs=22.5
Q ss_pred CCCCCccCCCCCCC-Ceeeeeccchhhhhccccc
Q psy6973 31 PGNLTCADCAEAGP-TWASLNLGLLLCIQCCGVH 63 (115)
Q Consensus 31 ~~N~~CaDCg~~~p-~waS~~~GvflC~~CsgiH 63 (115)
..--+|.+||.+=| .=.-..-+..+|..|...|
T Consensus 78 gtYG~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~ 111 (120)
T COG1734 78 GTYGICEECGEPIPEARLEARPTARLCIECQERA 111 (120)
T ss_pred CCccchhccCCcCCHHHHhhCcchHHHHHHHHHH
Confidence 34458999999855 2223444678999997654
No 52
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=55.27 E-value=3.3 Score=26.80 Aligned_cols=30 Identities=23% Similarity=0.591 Sum_probs=21.1
Q ss_pred CCCccCCCCCCCCe-eeeeccchhhhhcccc
Q psy6973 33 NLTCADCAEAGPTW-ASLNLGLLLCIQCCGV 62 (115)
Q Consensus 33 N~~CaDCg~~~p~w-aS~~~GvflC~~Csgi 62 (115)
..+|.|||.+=|.= .-.--|+..|..|...
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~ 64 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAY 64 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHH
Confidence 45899999986632 2233478899999764
No 53
>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=54.49 E-value=5.4 Score=27.29 Aligned_cols=30 Identities=23% Similarity=0.357 Sum_probs=18.8
Q ss_pred CCCCCccCCCCCCCC-eeeeeccchhhhhcc
Q psy6973 31 PGNLTCADCAEAGPT-WASLNLGLLLCIQCC 60 (115)
Q Consensus 31 ~~N~~CaDCg~~~p~-waS~~~GvflC~~Cs 60 (115)
+..-+|.+||.+=|. =.-.--+...|..|.
T Consensus 78 g~yG~C~~Cge~I~~~RL~a~P~a~~Cv~Cq 108 (110)
T TIGR02420 78 GEYGYCEECGEEIGLRRLEARPTATLCIDCK 108 (110)
T ss_pred CCCCchhccCCcccHHHHhhCCCccccHHhH
Confidence 566899999998441 111223455788875
No 54
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=53.57 E-value=15 Score=28.82 Aligned_cols=38 Identities=18% Similarity=0.306 Sum_probs=27.1
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhcccccc
Q psy6973 20 TASLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHR 64 (115)
Q Consensus 20 ~~~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR 64 (115)
++++++.....|.|. |--||.....|. ++|..|.+.|-
T Consensus 342 ~~~~~~~~~~~p~~~-c~~cg~~~~~~~------~~c~~c~~~~~ 379 (389)
T PRK11788 342 RDLVGEQLKRKPRYR-CRNCGFTARTLY------WHCPSCKAWET 379 (389)
T ss_pred HHHHHHHHhCCCCEE-CCCCCCCCccce------eECcCCCCccC
Confidence 334444444266654 999999999996 58999998763
No 55
>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=53.35 E-value=8.7 Score=26.55 Aligned_cols=31 Identities=19% Similarity=0.508 Sum_probs=25.3
Q ss_pred CCCCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 32 GNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 32 ~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
....|.-||.+... ..||+..|..|.+..|-
T Consensus 5 ~~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 35 (107)
T cd06955 5 VPRICGVCGDRATG---FHFNAMTCEGCKGFFRR 35 (107)
T ss_pred CCCCCeecCCcCcc---cEECcceeeeecceecc
Confidence 35779999986653 59999999999998774
No 56
>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=53.16 E-value=9 Score=25.44 Aligned_cols=30 Identities=23% Similarity=0.608 Sum_probs=24.2
Q ss_pred CCCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 33 NLTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 33 N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
...|.-||.+... ..||++.|..|.+..|-
T Consensus 3 ~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 32 (89)
T cd07166 3 VVLCKVCGDKASG---FHYGVHACEGCKGFFRR 32 (89)
T ss_pred CCCCcccCccCcc---eEEChhhhhhHhhEecc
Confidence 3569999986654 58999999999998764
No 57
>KOG3507|consensus
Probab=52.63 E-value=5.9 Score=25.05 Aligned_cols=24 Identities=21% Similarity=0.634 Sum_probs=15.8
Q ss_pred CCccCCCCCCCCeeeeeccchhhhhcc
Q psy6973 34 LTCADCAEAGPTWASLNLGLLLCIQCC 60 (115)
Q Consensus 34 ~~CaDCg~~~p~waS~~~GvflC~~Cs 60 (115)
-+|+|||+.+.- -.--++-|.+|+
T Consensus 21 YiCgdC~~en~l---k~~D~irCReCG 44 (62)
T KOG3507|consen 21 YICGDCGQENTL---KRGDVIRCRECG 44 (62)
T ss_pred EEeccccccccc---cCCCcEehhhcc
Confidence 468888887652 133467788874
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=51.67 E-value=7.3 Score=25.98 Aligned_cols=32 Identities=25% Similarity=0.636 Sum_probs=26.1
Q ss_pred CCCCCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 31 PGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 31 ~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
.....|.-||.+.. ...||+..|..|.+..|-
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 45778999998664 468999999999998763
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=51.33 E-value=8.5 Score=25.26 Aligned_cols=27 Identities=26% Similarity=0.712 Sum_probs=21.8
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|.-||.+.. ...||++.|..|.+..|-
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 777887655 358999999999998774
No 60
>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=50.73 E-value=9.2 Score=25.65 Aligned_cols=33 Identities=21% Similarity=0.597 Sum_probs=26.3
Q ss_pred CCCCCCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 30 VPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 30 ~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
++....|.-||.+... ..||+..|..|.+..|-
T Consensus 3 ~~p~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 35 (92)
T cd06970 3 LNPGLLCRVCGDTSSG---KHYGIYACNGCSGFFKR 35 (92)
T ss_pred CCCCCCCeecCCcCcc---cEECccEEeeeeeEeee
Confidence 3456679999987654 59999999999998764
No 61
>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=50.50 E-value=7.2 Score=23.68 Aligned_cols=33 Identities=27% Similarity=0.610 Sum_probs=25.6
Q ss_pred CccCCCCC-CCCeeeee-ccchhhhhccccccCCC
Q psy6973 35 TCADCAEA-GPTWASLN-LGLLLCIQCCGVHRCLG 67 (115)
Q Consensus 35 ~CaDCg~~-~p~waS~~-~GvflC~~CsgiHR~lG 67 (115)
.|..|+.. .|.|-... -+..||-.|.-..+..|
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC
Confidence 48899986 47898765 78899999987655544
No 62
>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=50.29 E-value=7.2 Score=25.29 Aligned_cols=29 Identities=21% Similarity=0.520 Sum_probs=23.5
Q ss_pred CCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 34 LTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 34 ~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
..|.-||.+.. ...||+..|..|.+..|-
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 46888997655 469999999999998763
No 63
>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=50.22 E-value=7.1 Score=24.30 Aligned_cols=26 Identities=23% Similarity=0.613 Sum_probs=20.3
Q ss_pred CCccCCCCCCCCeeeeeccchhhhhcccc
Q psy6973 34 LTCADCAEAGPTWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 34 ~~CaDCg~~~p~waS~~~GvflC~~Csgi 62 (115)
+.|.-||.+.+ ..+||+..|..|...
T Consensus 1 ~~C~VCg~~~~---~~~ygv~sC~~C~~F 26 (70)
T PF00105_consen 1 KKCKVCGDPAS---GYHYGVLSCNACKMF 26 (70)
T ss_dssp -BSTTTSSBES---EEETTEEEEHHHHHH
T ss_pred CCCeECCCccC---cccccccccccceee
Confidence 46888987543 469999999999984
No 64
>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=49.49 E-value=5.7 Score=29.28 Aligned_cols=41 Identities=20% Similarity=0.319 Sum_probs=25.8
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCC-Ceeeeeccchhhhhccccc
Q psy6973 21 ASLQSIRSRVPGNLTCADCAEAGP-TWASLNLGLLLCIQCCGVH 63 (115)
Q Consensus 21 ~~l~~l~~~~~~N~~CaDCg~~~p-~waS~~~GvflC~~CsgiH 63 (115)
+.|..|.. ..--+|.+||.+=| .=.-+--....|+.|...+
T Consensus 76 ~AL~Ri~~--G~YG~Ce~CGe~I~~~RL~a~P~a~~Ci~Cq~~~ 117 (159)
T TIGR02890 76 HALQKIEN--GTYGICEVCGKPIPYERLEAIPTATTCVECQNRK 117 (159)
T ss_pred HHHHHHhC--CCCCeecccCCcccHHHHhhCCCcchhHHHHHHh
Confidence 34444544 45668999998733 2222333567899998854
No 65
>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=49.38 E-value=7.3 Score=26.05 Aligned_cols=29 Identities=24% Similarity=0.545 Sum_probs=23.3
Q ss_pred CCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 34 LTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 34 ~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
..|.-||.+.. ...||+..|..|.+..|-
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 35888997665 459999999999998763
No 66
>PRK11019 hypothetical protein; Provisional
Probab=49.35 E-value=5.2 Score=26.94 Aligned_cols=32 Identities=25% Similarity=0.543 Sum_probs=22.4
Q ss_pred CCCCccCCCCCCCC-eeeeeccchhhhhccccc
Q psy6973 32 GNLTCADCAEAGPT-WASLNLGLLLCIQCCGVH 63 (115)
Q Consensus 32 ~N~~CaDCg~~~p~-waS~~~GvflC~~CsgiH 63 (115)
...+|.+||.+=|. =.-.--++..|..|...+
T Consensus 35 syg~C~~CG~~Ip~~Rl~A~P~a~~Cv~Cq~~~ 67 (88)
T PRK11019 35 SLTECEECGEPIPEARRKAIPGVRLCVACQQEK 67 (88)
T ss_pred cCCeeCcCCCcCcHHHHhhcCCccccHHHHHHH
Confidence 45799999998663 112233788999998754
No 67
>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=48.74 E-value=9.1 Score=25.27 Aligned_cols=28 Identities=25% Similarity=0.581 Sum_probs=22.8
Q ss_pred CccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 35 TCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 35 ~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
.|.-||.+.. ...||+..|..|.+..|-
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 4888987664 459999999999998764
No 68
>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=48.56 E-value=9.4 Score=25.11 Aligned_cols=29 Identities=24% Similarity=0.545 Sum_probs=23.1
Q ss_pred CCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 34 LTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 34 ~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
..|.-||.+... ..||+..|..|.+..|-
T Consensus 2 ~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 30 (84)
T cd06962 2 ELCVVCGDKASG---YHYNALTCEGCKGFFRR 30 (84)
T ss_pred CCCeecCCcCcc---eEECcceeecceeeeee
Confidence 358888876653 59999999999998763
No 69
>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=47.55 E-value=9 Score=23.54 Aligned_cols=28 Identities=18% Similarity=0.399 Sum_probs=23.1
Q ss_pred CCCCccCCCCCCCCeeeeeccchhhhhccc
Q psy6973 32 GNLTCADCAEAGPTWASLNLGLLLCIQCCG 61 (115)
Q Consensus 32 ~N~~CaDCg~~~p~waS~~~GvflC~~Csg 61 (115)
-.+.|..||..... ..+..+|.|..|..
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 46889999998887 66778999999865
No 70
>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=47.30 E-value=1.2 Score=24.71 Aligned_cols=28 Identities=32% Similarity=0.663 Sum_probs=15.1
Q ss_pred CccCCCCCCCC-eeeeeccchhhhhcccc
Q psy6973 35 TCADCAEAGPT-WASLNLGLLLCIQCCGV 62 (115)
Q Consensus 35 ~CaDCg~~~p~-waS~~~GvflC~~Csgi 62 (115)
.|.+||.+=|. -.-+.-+..+|..|+..
T Consensus 5 ~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 5 ICEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp B-TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred CccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 48888876432 11223367788888754
No 71
>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=46.31 E-value=12 Score=24.85 Aligned_cols=32 Identities=22% Similarity=0.614 Sum_probs=25.5
Q ss_pred CCCCCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 31 PGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 31 ~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
.....|.-||.+.. ...||+..|..|.+..|-
T Consensus 4 ~~~~~C~VCg~~~~---g~hyGv~sC~aCk~FFRR 35 (90)
T cd07168 4 ESPKLCSICEDKAT---GLHYGIITCEGCKGFFKR 35 (90)
T ss_pred ccCCCCcccCCcCc---ceEECceehhhhhHhhhh
Confidence 34567999998654 469999999999998764
No 72
>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=45.77 E-value=11 Score=23.96 Aligned_cols=27 Identities=22% Similarity=0.645 Sum_probs=20.9
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|.-||.+... ..||+..|..|.+..|-
T Consensus 1 C~VC~~~~~g---~hygv~sC~aC~~FFRR 27 (72)
T cd07156 1 CGVCGDRATG---YHFNAMTCEGCKGFFRR 27 (72)
T ss_pred CCccCccCcc---cEECcceehhhhhhhch
Confidence 5567766554 59999999999998764
No 73
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=45.71 E-value=8.3 Score=25.44 Aligned_cols=28 Identities=21% Similarity=0.602 Sum_probs=22.2
Q ss_pred CccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 35 TCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 35 ~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
.|.-||.+... ..||+..|..|.+..|-
T Consensus 1 ~C~VCg~~~~g---~hygv~sC~aC~~FFRR 28 (87)
T cd07162 1 ICRVCGDRATG---YHFNAMTCEGCKGFFRR 28 (87)
T ss_pred CCcccCCcCcc---eEECcceehhhHHHHHh
Confidence 37778876654 58999999999997763
No 74
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=45.30 E-value=6.6 Score=28.73 Aligned_cols=41 Identities=17% Similarity=0.275 Sum_probs=25.6
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCC-Ceeeeeccchhhhhccccc
Q psy6973 21 ASLQSIRSRVPGNLTCADCAEAGP-TWASLNLGLLLCIQCCGVH 63 (115)
Q Consensus 21 ~~l~~l~~~~~~N~~CaDCg~~~p-~waS~~~GvflC~~CsgiH 63 (115)
+.|..|.. +..-+|-+||.+=| .=.-+--+...|+.|...+
T Consensus 101 ~AL~Ri~~--gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~ 142 (151)
T PRK10778 101 KTLKKVED--EDFGYCESCGVEIGIRRLEARPTADLCIDCKTLA 142 (151)
T ss_pred HHHHHHhC--CCCceeccCCCcccHHHHhcCCCccccHHHHHHH
Confidence 34444443 77889999998843 2222333556899997754
No 75
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=44.70 E-value=28 Score=23.63 Aligned_cols=33 Identities=18% Similarity=0.431 Sum_probs=25.5
Q ss_pred CCCCCCccCCCCCCCCeeeeeccchhhhhcccccc
Q psy6973 30 VPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHR 64 (115)
Q Consensus 30 ~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR 64 (115)
.-.--.|..|+.+ .---+..||..|..|...-.
T Consensus 32 ~~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 32 QRAKHVCPFCGRT--TVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred HhcCCcCCCCCCc--ceeeeccCeEEcCCCCCeec
Confidence 3446789999998 44567899999999987543
No 76
>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=44.56 E-value=12 Score=23.76 Aligned_cols=27 Identities=19% Similarity=0.573 Sum_probs=20.7
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|.-||.+.. ...||+..|..|.+..|-
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 556776555 359999999999998764
No 77
>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=44.33 E-value=22 Score=20.43 Aligned_cols=38 Identities=24% Similarity=0.496 Sum_probs=26.1
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhcc
Q psy6973 20 TASLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCC 60 (115)
Q Consensus 20 ~~~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~Cs 60 (115)
.++|.+++= |+.-+|.-||.....+.. +.+.+-|.+|.
T Consensus 7 ~~~l~~~RW--~~g~~CP~Cg~~~~~~~~-~~~~~~C~~C~ 44 (46)
T PF12760_consen 7 REYLEEIRW--PDGFVCPHCGSTKHYRLK-TRGRYRCKACR 44 (46)
T ss_pred HHHHHHhcC--CCCCCCCCCCCeeeEEeC-CCCeEECCCCC
Confidence 445555554 666889999998554433 35888888884
No 78
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=44.05 E-value=10 Score=24.05 Aligned_cols=27 Identities=26% Similarity=0.685 Sum_probs=20.9
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|.-||.+... ..||++.|..|.+..|-
T Consensus 1 C~VCg~~~~g---~hyGv~~C~aC~~FFRR 27 (73)
T cd07158 1 CKVCGDKASG---FHYGVHSCEGCKGFFRR 27 (73)
T ss_pred CcccCccCcc---eEECcchhhHHHHHHhh
Confidence 5567765553 58999999999998764
No 79
>cd06964 NR_DBD_RAR DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter reg
Probab=43.77 E-value=13 Score=24.50 Aligned_cols=30 Identities=23% Similarity=0.552 Sum_probs=24.1
Q ss_pred CCCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 33 NLTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 33 N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
...|.-||.+.. ...||+..|..|.+..|-
T Consensus 4 ~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 33 (85)
T cd06964 4 YKPCFVCQDKSS---GYHYGVSACEGCKGFFRR 33 (85)
T ss_pred CCCCcccCCcCc---ccEECcceeeeeeeEEee
Confidence 356889998655 458999999999998764
No 80
>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=43.53 E-value=12 Score=24.74 Aligned_cols=30 Identities=20% Similarity=0.492 Sum_probs=24.0
Q ss_pred CCCccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 33 NLTCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 33 N~~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
...|.-||.+... ..||+..|..|.+..|-
T Consensus 3 ~~~C~VCg~~~~g---~hyGv~sC~aC~~FFRR 32 (87)
T cd06967 3 VELCVVCGDKASG---RHYGAVSCEGCKGFFKR 32 (87)
T ss_pred CCCCeecCCcCCc---CEeCcceEeeeeeEeee
Confidence 3568899986654 48999999999998763
No 81
>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=43.18 E-value=9.7 Score=24.34 Aligned_cols=27 Identities=19% Similarity=0.583 Sum_probs=20.8
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|+-||.+.. ...||+..|..|.+..|-
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 556776644 469999999999998763
No 82
>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=42.59 E-value=9.1 Score=24.63 Aligned_cols=28 Identities=25% Similarity=0.642 Sum_probs=22.5
Q ss_pred CccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 35 TCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 35 ~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
.|.-||.+.. ...||+..|..|.+..|-
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 5788887665 459999999999998763
No 83
>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=42.15 E-value=13 Score=23.74 Aligned_cols=27 Identities=33% Similarity=0.753 Sum_probs=20.8
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 1 C~vCg~~~~---~~hygv~~C~aC~~FFrR 27 (76)
T cd06960 1 CAVCGDRAT---GKHYGVLSCNGCKGFFRR 27 (76)
T ss_pred CCccCccCc---ccEECcceeeeehheeCc
Confidence 556776654 458999999999998764
No 84
>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=40.50 E-value=7 Score=25.65 Aligned_cols=15 Identities=33% Similarity=0.751 Sum_probs=12.2
Q ss_pred ccchhhhhccccccC
Q psy6973 51 LGLLLCIQCCGVHRC 65 (115)
Q Consensus 51 ~GvflC~~CsgiHR~ 65 (115)
.|++.|.+|.||.-.
T Consensus 2 ~G~LPCADC~GI~t~ 16 (87)
T PF04170_consen 2 EGTLPCADCPGIKTT 16 (87)
T ss_dssp EEEEEETTSSEEEEE
T ss_pred ccEeECCCCCCeEEE
Confidence 489999999998643
No 85
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=40.22 E-value=18 Score=24.72 Aligned_cols=32 Identities=28% Similarity=0.571 Sum_probs=22.8
Q ss_pred CCCCCCccCCCCCC---C-----Ce---------eeeeccchhhhhccc
Q psy6973 30 VPGNLTCADCAEAG---P-----TW---------ASLNLGLLLCIQCCG 61 (115)
Q Consensus 30 ~~~N~~CaDCg~~~---p-----~w---------aS~~~GvflC~~Csg 61 (115)
.++--.|++||.+- | ++ .+-.||-.+|..|..
T Consensus 31 ~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 31 KPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred cCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 67778999999761 1 11 245688899998864
No 86
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=40.16 E-value=16 Score=25.66 Aligned_cols=24 Identities=38% Similarity=0.681 Sum_probs=20.5
Q ss_pred Ceeeeecc--chhhhhccccccCCCc
Q psy6973 45 TWASLNLG--LLLCIQCCGVHRCLGA 68 (115)
Q Consensus 45 ~waS~~~G--vflC~~CsgiHR~lG~ 68 (115)
.|.+-.-| |..|.+|-=+|+.-++
T Consensus 52 ewi~~~~G~~VwSC~dC~~iH~ke~~ 77 (112)
T COG2158 52 EWISDSNGRKVWSCSDCHWIHRKEGA 77 (112)
T ss_pred ceeEcCCCCEEeeccccceecccchH
Confidence 88888889 9999999999997554
No 87
>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=40.13 E-value=13 Score=24.24 Aligned_cols=26 Identities=19% Similarity=0.580 Sum_probs=20.1
Q ss_pred ccCCCCCCCCeeeeeccchhhhhcccccc
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHR 64 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR 64 (115)
|.-||.+.. ...||+..|..|.+..|
T Consensus 1 C~VCg~~~~---g~hyGv~sC~aCk~FFR 26 (82)
T cd06957 1 CKVCGDKSY---GKHYGVYCCDGCSCFFK 26 (82)
T ss_pred CCccCccCc---ceEECcceEeeeeeEEE
Confidence 555776555 45999999999999865
No 88
>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=39.74 E-value=13 Score=24.40 Aligned_cols=27 Identities=22% Similarity=0.597 Sum_probs=21.4
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|.-||.+... ..||+..|..|.+..|-
T Consensus 2 C~VCg~~~~g---~hygv~sC~aC~~FFRR 28 (85)
T cd06961 2 CVVCGDKATG---YHYRCITCEGCKGFFRR 28 (85)
T ss_pred CceeCCcCcc---eEEChhhhhhhhHhhHh
Confidence 6778876553 58999999999998763
No 89
>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=39.18 E-value=13 Score=23.74 Aligned_cols=27 Identities=22% Similarity=0.573 Sum_probs=20.6
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|.-||.+.. ...||++.|..|.+..|-
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 469999999999998763
No 90
>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=38.87 E-value=11 Score=24.13 Aligned_cols=26 Identities=31% Similarity=0.764 Sum_probs=20.4
Q ss_pred ccCCCCCCCCeeeeeccchhhhhcccccc
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHR 64 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR 64 (115)
|.-||.+... ..||+..|..|.+..|
T Consensus 1 C~VCg~~~~g---~hygv~sC~aC~~FFR 26 (74)
T cd07179 1 CRVCGGKSSG---FHFGALTCEGCKGFFR 26 (74)
T ss_pred CcccCccCcc---eEECceeehhHHHHHH
Confidence 5567766553 5899999999999776
No 91
>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=38.78 E-value=12 Score=24.23 Aligned_cols=27 Identities=26% Similarity=0.687 Sum_probs=21.0
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|.-||.+.. ...||+..|..|.+..|-
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 556776554 459999999999998774
No 92
>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=38.77 E-value=13 Score=23.46 Aligned_cols=31 Identities=32% Similarity=0.562 Sum_probs=23.4
Q ss_pred ccC-CCCCCCC-eeeeeccchhhhhccccccCCC
Q psy6973 36 CAD-CAEAGPT-WASLNLGLLLCIQCCGVHRCLG 67 (115)
Q Consensus 36 CaD-Cg~~~p~-waS~~~GvflC~~CsgiHR~lG 67 (115)
..| |+...|. +..-+...+.|..| |-||+|=
T Consensus 21 a~DGCgEFm~~~g~eg~~~al~CaAC-gCHRnFH 53 (60)
T PF04770_consen 21 AVDGCGEFMPSPGEEGTPEALKCAAC-GCHRNFH 53 (60)
T ss_pred ccccccccccCCCCCCCcccceeccc-Ccchhcc
Confidence 445 8888887 66667888999988 5588873
No 93
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=38.63 E-value=14 Score=23.11 Aligned_cols=27 Identities=22% Similarity=0.659 Sum_probs=21.4
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|.-||.+... ..||+..|..|.+..|-
T Consensus 2 C~vC~~~~~~---~hygv~~C~aC~~FFRR 28 (70)
T smart00399 2 CCVCGDHASG---FHFGVCSCRACKAFFRR 28 (70)
T ss_pred CeEeCCcCcc---cEeCCcEechhhhhhhh
Confidence 6678776654 48999999999998763
No 94
>PHA00080 DksA-like zinc finger domain containing protein
Probab=38.54 E-value=5.5 Score=25.64 Aligned_cols=32 Identities=22% Similarity=0.588 Sum_probs=21.4
Q ss_pred CCCCCccCCCCCCCCe-eeeeccchhhhhcccc
Q psy6973 31 PGNLTCADCAEAGPTW-ASLNLGLLLCIQCCGV 62 (115)
Q Consensus 31 ~~N~~CaDCg~~~p~w-aS~~~GvflC~~Csgi 62 (115)
++..+|.+||.+=|.= .-..-++..|..|...
T Consensus 29 ~~~~~C~~Cg~~Ip~~Rl~a~P~~~~Cv~Cq~~ 61 (72)
T PHA00080 29 PSATHCEECGDPIPEARREAVPGCRTCVSCQEI 61 (72)
T ss_pred CCCCEecCCCCcCcHHHHHhCCCccCcHHHHHH
Confidence 4466899999986521 1123467789999774
No 95
>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=37.62 E-value=16 Score=23.13 Aligned_cols=27 Identities=22% Similarity=0.682 Sum_probs=20.7
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 1 C~vCg~~~~---~~hyGv~sC~aC~~FFRR 27 (73)
T cd07154 1 CKVCGDRSS---GKHYGVYACDGCSGFFKR 27 (73)
T ss_pred CcccCccCc---ceEECcceeeeeeeEeee
Confidence 555776554 359999999999998764
No 96
>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=36.96 E-value=18 Score=23.23 Aligned_cols=27 Identities=22% Similarity=0.594 Sum_probs=20.7
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|.-||.+... ..||+..|..|.+..|-
T Consensus 1 C~VCg~~~~g---~hyG~~~C~~C~~FFRR 27 (78)
T cd07164 1 CRVCGDRASG---KHYGVPSCDGCRGFFKR 27 (78)
T ss_pred CcccCccCcc---eEECcchhhhhhhhhhh
Confidence 5567765543 59999999999998764
No 97
>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=36.94 E-value=16 Score=23.10 Aligned_cols=27 Identities=33% Similarity=0.796 Sum_probs=20.4
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 1 C~vC~~~~~---~~hygv~sC~aC~~FFRR 27 (72)
T cd06916 1 CAVCGDKAS---GYHYGVLTCEGCKGFFRR 27 (72)
T ss_pred CCccCccCc---ccEECcceeeeeeeeEeE
Confidence 455776554 468999999999998763
No 98
>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=36.79 E-value=7.9 Score=20.32 Aligned_cols=28 Identities=18% Similarity=0.287 Sum_probs=15.8
Q ss_pred CCccCCCCCCCCeeeeeccchhhhhccc
Q psy6973 34 LTCADCAEAGPTWASLNLGLLLCIQCCG 61 (115)
Q Consensus 34 ~~CaDCg~~~p~waS~~~GvflC~~Csg 61 (115)
+.|.-|+..-++-.......++|..|..
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 3577777776655555667788888854
No 99
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=36.78 E-value=34 Score=23.72 Aligned_cols=43 Identities=16% Similarity=0.287 Sum_probs=27.9
Q ss_pred ChHHHHHHHHHHhcCCCCCCccCCCCCCCCeeeeecc-chhhhhccc
Q psy6973 16 SSVETASLQSIRSRVPGNLTCADCAEAGPTWASLNLG-LLLCIQCCG 61 (115)
Q Consensus 16 ~~~~~~~l~~l~~~~~~N~~CaDCg~~~p~waS~~~G-vflC~~Csg 61 (115)
+..-++.|+...+ .--.|-.|+.|+..-.--+-- ...|..|++
T Consensus 66 ~~~i~~~l~~yI~---~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 66 PKKLQDLLRRYIK---EYVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred HHHHHHHHHHHHH---hcEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 3444556666555 467899999999877653332 344777764
No 100
>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=36.55 E-value=18 Score=23.15 Aligned_cols=28 Identities=25% Similarity=0.632 Sum_probs=22.0
Q ss_pred CccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 35 TCADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 35 ~CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
.|.-||.+.. ...||+..|..|.+..|-
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 358999999999998764
No 101
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=36.53 E-value=25 Score=20.06 Aligned_cols=22 Identities=27% Similarity=0.721 Sum_probs=15.0
Q ss_pred CccCCCCCCCCeeeeeccchhh
Q psy6973 35 TCADCAEAGPTWASLNLGLLLC 56 (115)
Q Consensus 35 ~CaDCg~~~p~waS~~~GvflC 56 (115)
.|.+|+..+.-|+.+.-+...|
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c 22 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGC 22 (50)
T ss_pred CcccCCCcCCeEEecCCCCccc
Confidence 4889998887776655554444
No 102
>KOG1597|consensus
Probab=36.25 E-value=21 Score=29.20 Aligned_cols=28 Identities=29% Similarity=0.536 Sum_probs=23.5
Q ss_pred CccCCCCCCC-Ceeeeeccchhhhhcccc
Q psy6973 35 TCADCAEAGP-TWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 35 ~CaDCg~~~p-~waS~~~GvflC~~Csgi 62 (115)
.|.||....+ .-.....|..+|..|+-+
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlV 30 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTVCSECGLV 30 (308)
T ss_pred CCCCCCCCCCCeeeeccCCceecccCCee
Confidence 6999999887 555678899999999875
No 103
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=36.24 E-value=13 Score=21.72 Aligned_cols=24 Identities=17% Similarity=0.541 Sum_probs=16.8
Q ss_pred CccCCCCCCCCeeeeeccchhhhhccc
Q psy6973 35 TCADCAEAGPTWASLNLGLLLCIQCCG 61 (115)
Q Consensus 35 ~CaDCg~~~p~waS~~~GvflC~~Csg 61 (115)
.|.+||...... ..+..-|..|+.
T Consensus 4 ~C~~Cg~~~~~~---~~~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIK---SKDVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecC---CCCceECCCCCc
Confidence 589999865432 456778888854
No 104
>PF14376 Haem_bd: Haem-binding domain
Probab=35.90 E-value=32 Score=24.40 Aligned_cols=25 Identities=16% Similarity=0.377 Sum_probs=17.5
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCeeee
Q psy6973 20 TASLQSIRSRVPGNLTCADCAEAGPTWASL 49 (115)
Q Consensus 20 ~~~l~~l~~~~~~N~~CaDCg~~~p~waS~ 49 (115)
.+.++.|.+ +-|.||++.++.|.-+
T Consensus 33 p~~v~~il~-----~~CydCHSn~T~~PwY 57 (137)
T PF14376_consen 33 PEEVKIILK-----NSCYDCHSNNTRYPWY 57 (137)
T ss_pred hHHHHHHHH-----ccccccCCCCCCCccc
Confidence 334455555 6799999999887643
No 105
>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=35.86 E-value=14 Score=23.47 Aligned_cols=27 Identities=30% Similarity=0.783 Sum_probs=21.3
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 2 C~vCg~~~~---~~hygv~sC~aC~~FFRR 28 (73)
T cd06959 2 CVVCGDKAS---GFHYGVLSCEGCKGFFRR 28 (73)
T ss_pred CceeCCcCc---ceEECceeehhhHHHHHH
Confidence 667876555 459999999999998763
No 106
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=35.28 E-value=38 Score=25.65 Aligned_cols=75 Identities=13% Similarity=0.177 Sum_probs=42.7
Q ss_pred ChHHHHHHHHHHhcCCCCCCccCCCCCCCCeeeee-ccchhhhhccccccCCCceeeEEEecC---CCcccch-----hh
Q psy6973 16 SSVETASLQSIRSRVPGNLTCADCAEAGPTWASLN-LGLLLCIQCCGVHRCLGAHVSRVRSLE---LDEWPLN-----LG 86 (115)
Q Consensus 16 ~~~~~~~l~~l~~~~~~N~~CaDCg~~~p~waS~~-~GvflC~~CsgiHR~lG~~is~VkSl~---ld~W~~~-----~~ 86 (115)
+..-++.|+...+ .-=.|..|+.|+..-.--+ .-...|..|++ +|... .+++.+ .+.+... .+
T Consensus 84 ~~~i~~~l~~yi~---~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa-~~~v~----~~~~~~~~~~~~~~~~e~~~v~I 155 (201)
T PRK12336 84 EEDIQAAIDAYVD---EYVICSECGLPDTRLVKEDRVLMLRCDACGA-HRPVK----KRKASSETQREAIEEGKTYEVEI 155 (201)
T ss_pred HHHHHHHHHHHHH---heEECCCCCCCCcEEEEcCCeEEEEcccCCC-Ccccc----ccccccCCCCCCCccCCEEEEEE
Confidence 3444555555555 4678999999998776422 22457888866 44433 333332 1222221 24
Q ss_pred hhhhhhccCccc
Q psy6973 87 LLLCIQCCGVHR 98 (115)
Q Consensus 87 ~~m~~~gng~~r 98 (115)
+.+...|.|..+
T Consensus 156 e~l~~~G~GVak 167 (201)
T PRK12336 156 TGTGRKGDGVAK 167 (201)
T ss_pred EEccCCCceEEE
Confidence 556667777665
No 107
>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=34.16 E-value=14 Score=20.26 Aligned_cols=24 Identities=17% Similarity=0.458 Sum_probs=13.8
Q ss_pred CccCCCCCCCCeeeeeccchhhhhccc
Q psy6973 35 TCADCAEAGPTWASLNLGLLLCIQCCG 61 (115)
Q Consensus 35 ~CaDCg~~~p~waS~~~GvflC~~Csg 61 (115)
.|.+||+...- . .....-|..|+.
T Consensus 2 ~C~~Cg~~~~~--~-~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVEL--K-PGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-B--S-TSSTSSBSSSS-
T ss_pred CCCcCCCeeEc--C-CCCcEECCcCCC
Confidence 58889887651 1 234457777753
No 108
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=33.62 E-value=51 Score=22.32 Aligned_cols=39 Identities=15% Similarity=0.379 Sum_probs=28.2
Q ss_pred HHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhcccc
Q psy6973 22 SLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 22 ~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~Csgi 62 (115)
.+.+|..+...--.|.-||....... ..||.-|..|.-.
T Consensus 25 ~v~kie~~q~a~y~CpfCgk~~vkR~--a~GIW~C~~C~~~ 63 (90)
T PTZ00255 25 QIKKIEISQHAKYFCPFCGKHAVKRQ--AVGIWRCKGCKKT 63 (90)
T ss_pred HHHHHHHHHhCCccCCCCCCCceeee--eeEEEEcCCCCCE
Confidence 44555554567889999997776554 4599999999654
No 109
>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=31.75 E-value=17 Score=19.77 Aligned_cols=27 Identities=26% Similarity=0.603 Sum_probs=17.3
Q ss_pred CccCCCCCCCCeeeee-ccchhhhhccc
Q psy6973 35 TCADCAEAGPTWASLN-LGLLLCIQCCG 61 (115)
Q Consensus 35 ~CaDCg~~~p~waS~~-~GvflC~~Csg 61 (115)
.|.+||..-..+.+.. -....|-.|++
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 5777887655555543 44566777766
No 110
>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=30.34 E-value=19 Score=24.21 Aligned_cols=27 Identities=30% Similarity=0.741 Sum_probs=20.7
Q ss_pred ccCCCCCCCCeeeeeccchhhhhccccccC
Q psy6973 36 CADCAEAGPTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 36 CaDCg~~~p~waS~~~GvflC~~CsgiHR~ 65 (115)
|.-|+.+.. ...||+..|..|.+..|-
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 556776554 369999999999997753
No 111
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=30.27 E-value=38 Score=24.58 Aligned_cols=32 Identities=25% Similarity=0.499 Sum_probs=23.1
Q ss_pred CCCCCCccCCCCCC-----------------CCeeeeeccchhhhhccc
Q psy6973 30 VPGNLTCADCAEAG-----------------PTWASLNLGLLLCIQCCG 61 (115)
Q Consensus 30 ~~~N~~CaDCg~~~-----------------p~waS~~~GvflC~~Csg 61 (115)
.+.--.|.|||.+- -.-++-.||-.+|..|.-
T Consensus 38 ~~~~pkC~~cg~~L~GI~~~Rp~e~~rlsK~~KtvsRaYGG~lC~~CVr 86 (135)
T PTZ00074 38 KSSGPKCGDCGKVLAGIKALRPTEYKQLSRRERTVSRAYGGVLCHKCVR 86 (135)
T ss_pred CCCCCCCCCCCCccCCccCCchHHHHHccccCCCccCCCccchhHHHHH
Confidence 45566799999762 123467889999999964
No 112
>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=30.23 E-value=27 Score=18.18 Aligned_cols=14 Identities=21% Similarity=0.695 Sum_probs=8.0
Q ss_pred CCCCCccCCCCCCC
Q psy6973 31 PGNLTCADCAEAGP 44 (115)
Q Consensus 31 ~~N~~CaDCg~~~p 44 (115)
+.+..|.-|+++.|
T Consensus 16 ~~~~~C~~C~~~rp 29 (30)
T PF00641_consen 16 ASRSKCVACGAPRP 29 (30)
T ss_dssp SSSSB-TTT--BTT
T ss_pred HHhhhhhCcCCCCc
Confidence 45677888888776
No 113
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=29.97 E-value=23 Score=19.82 Aligned_cols=28 Identities=18% Similarity=0.490 Sum_probs=17.2
Q ss_pred CccCCCCCCCCeeeeeccchhhhhcccc
Q psy6973 35 TCADCAEAGPTWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 35 ~CaDCg~~~p~waS~~~GvflC~~Csgi 62 (115)
.|..|+..-..-.--.+-+..|..|.|+
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeE
Confidence 3667776544333344567778888775
No 114
>COG2124 CypX Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=28.52 E-value=17 Score=29.85 Aligned_cols=19 Identities=42% Similarity=0.632 Sum_probs=14.8
Q ss_pred hhhhccCcccccCccccce
Q psy6973 89 LCIQCCGVHRCLGAHVSRV 107 (115)
Q Consensus 89 m~~~gng~~r~~g~~is~~ 107 (115)
...=|.|.|+|+|.++++.
T Consensus 349 ~l~FG~G~H~ClG~~lA~~ 367 (411)
T COG2124 349 HLPFGGGPHRCLGAALARL 367 (411)
T ss_pred CcCCCCCCccccCHHHHHH
Confidence 4445789999999998653
No 115
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=27.91 E-value=29 Score=19.88 Aligned_cols=30 Identities=13% Similarity=0.246 Sum_probs=18.5
Q ss_pred CCccCCCCCC--CCeeeeeccchhhhhccccccC
Q psy6973 34 LTCADCAEAG--PTWASLNLGLLLCIQCCGVHRC 65 (115)
Q Consensus 34 ~~CaDCg~~~--p~waS~~~GvflC~~CsgiHR~ 65 (115)
+.|.+||..- +.+.. --.++|..|.-.++.
T Consensus 1 ~FCp~Cg~~l~~~~~~~--~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 1 KFCPKCGNMLIPKEGKE--KRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCCccccccCCC--CCEEECCcCCCeEEC
Confidence 4789999753 22221 126789999865543
No 116
>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=26.85 E-value=37 Score=20.16 Aligned_cols=29 Identities=24% Similarity=0.685 Sum_probs=19.2
Q ss_pred CCCccCCCCCCC--Cee-------eeeccchhhhhccc
Q psy6973 33 NLTCADCAEAGP--TWA-------SLNLGLLLCIQCCG 61 (115)
Q Consensus 33 N~~CaDCg~~~p--~wa-------S~~~GvflC~~Csg 61 (115)
+..|-=|++..+ .|. +....|++|..|..
T Consensus 7 ~~kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 7 ESKCELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHS 44 (47)
T ss_pred CCcccCcCCCCCceEEecCCCCCCCccceeeechHHHH
Confidence 445999998654 222 23557899998864
No 117
>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=26.64 E-value=31 Score=23.49 Aligned_cols=31 Identities=29% Similarity=0.550 Sum_probs=16.8
Q ss_pred CCCCCCccCCCCCCC-----------------Ceeeeeccchhhhhcc
Q psy6973 30 VPGNLTCADCAEAGP-----------------TWASLNLGLLLCIQCC 60 (115)
Q Consensus 30 ~~~N~~CaDCg~~~p-----------------~waS~~~GvflC~~Cs 60 (115)
.+.-..|+|||.+-. .-++-.||-.+|..|-
T Consensus 38 ~~~~pkC~~cg~~L~Gi~~~rp~~~~rl~k~~k~vsRaYGG~lc~~cv 85 (94)
T PF01199_consen 38 KPKKPKCGDCGKPLNGIPALRPVELRRLSKRQKTVSRAYGGSLCHKCV 85 (94)
T ss_dssp -TT--BSTSSS-BSSSS-SS-SSTTGTS-CHCH--CCTSSSS-HHHHH
T ss_pred cCCCCCcCccCCcccccccccHHHHhhcccCCCCCCCCCCccchHHHH
Confidence 344456999997522 1235678888888884
No 118
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=26.63 E-value=41 Score=22.80 Aligned_cols=39 Identities=18% Similarity=0.435 Sum_probs=27.4
Q ss_pred HHHHHHhcCCCCCCccCCCCCCCCeeeeeccchhhhhcccc
Q psy6973 22 SLQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 22 ~l~~l~~~~~~N~~CaDCg~~~p~waS~~~GvflC~~Csgi 62 (115)
.+.+|..+....-.|..||..... -...||+-|..|.-.
T Consensus 24 ~vkkie~~q~~ky~Cp~Cgk~~vk--R~a~GIW~C~~C~~~ 62 (90)
T PF01780_consen 24 RVKKIEISQHAKYTCPFCGKTSVK--RVATGIWKCKKCGKK 62 (90)
T ss_dssp HHHHHHHHHHS-BEESSSSSSEEE--EEETTEEEETTTTEE
T ss_pred HHHHHHHHHhCCCcCCCCCCceeE--EeeeEEeecCCCCCE
Confidence 334444434568899999998843 468899999999754
No 119
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=26.12 E-value=31 Score=26.26 Aligned_cols=25 Identities=32% Similarity=0.529 Sum_probs=20.3
Q ss_pred CCCCCccCCCCCCCCeeeeeccchhhhhcccc
Q psy6973 31 PGNLTCADCAEAGPTWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 31 ~~N~~CaDCg~~~p~waS~~~GvflC~~Csgi 62 (115)
+-.+.|.-||. ..-+.+.|..|...
T Consensus 307 ~tS~~C~~cg~-------~~~r~~~C~~cg~~ 331 (364)
T COG0675 307 YTSKTCPCCGH-------LSGRLFKCPRCGFV 331 (364)
T ss_pred CCcccccccCC-------ccceeEECCCCCCe
Confidence 34589999999 55788999999874
No 120
>PHA02942 putative transposase; Provisional
Probab=25.74 E-value=31 Score=28.64 Aligned_cols=28 Identities=14% Similarity=0.432 Sum_probs=21.0
Q ss_pred CCCCccCCCCCCCCeeeeeccchhhhhcccc
Q psy6973 32 GNLTCADCAEAGPTWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 32 ~N~~CaDCg~~~p~waS~~~GvflC~~Csgi 62 (115)
-.+.|..||...+ ..+-.+|.|..|+-.
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 234568999999764
No 121
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.26 E-value=29 Score=23.96 Aligned_cols=31 Identities=23% Similarity=0.377 Sum_probs=20.7
Q ss_pred CCCCCCccCCCCCCCCeeeeeccchhhhhccccc
Q psy6973 30 VPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVH 63 (115)
Q Consensus 30 ~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiH 63 (115)
.|.--.|.+||..-| ...+..+.|..|.+..
T Consensus 67 ~p~~~~C~~Cg~~~~---~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 67 QEAECWCETCQQYVT---LLTQRVRRCPQCHGDM 97 (114)
T ss_pred eCcEEEcccCCCeee---cCCccCCcCcCcCCCC
Confidence 356678999996332 3344457899998754
No 122
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=25.00 E-value=34 Score=18.77 Aligned_cols=29 Identities=21% Similarity=0.404 Sum_probs=20.5
Q ss_pred CCCccCCCCCCCCeeeeeccchhhhhccccc
Q psy6973 33 NLTCADCAEAGPTWASLNLGLLLCIQCCGVH 63 (115)
Q Consensus 33 N~~CaDCg~~~p~waS~~~GvflC~~CsgiH 63 (115)
.+.|-.|+.+.--+ -.-+..+|..|..++
T Consensus 3 ~~~C~~C~~~~i~~--~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVN--KEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEE--ecCCeEEcccCCcEe
Confidence 45687888877543 467788888887653
No 123
>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=24.83 E-value=30 Score=20.05 Aligned_cols=27 Identities=22% Similarity=0.534 Sum_probs=18.4
Q ss_pred CccCCCCCCCCeeeeec-cchhhhhccc
Q psy6973 35 TCADCAEAGPTWASLNL-GLLLCIQCCG 61 (115)
Q Consensus 35 ~CaDCg~~~p~waS~~~-GvflC~~Csg 61 (115)
.|.+||..-..|.+..- ....|-.|.+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 58888886666765443 4556888876
No 124
>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=24.49 E-value=26 Score=26.49 Aligned_cols=28 Identities=25% Similarity=0.601 Sum_probs=20.6
Q ss_pred CccCCCCCCC----Ceeeeeccchhhhhcccc
Q psy6973 35 TCADCAEAGP----TWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 35 ~CaDCg~~~p----~waS~~~GvflC~~Csgi 62 (115)
+|.+||.+.+ ++.+-+.-...|.+|..+
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~v 33 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCGKV 33 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccCCc
Confidence 6999999964 454555667889998764
No 125
>PRK10523 lipoprotein involved with copper homeostasis and adhesion; Provisional
Probab=24.44 E-value=34 Score=26.90 Aligned_cols=20 Identities=25% Similarity=0.522 Sum_probs=16.7
Q ss_pred Ceeeeeccchhhhhcccccc
Q psy6973 45 TWASLNLGLLLCIQCCGVHR 64 (115)
Q Consensus 45 ~waS~~~GvflC~~CsgiHR 64 (115)
.|.-.-.|++.|.+|.||--
T Consensus 40 p~~gtY~G~LPCADC~GI~t 59 (234)
T PRK10523 40 PMQQSWRGVLPCADCEGIET 59 (234)
T ss_pred ccccEEeEEEECCCCCCceE
Confidence 57778889999999999743
No 126
>PF12773 DZR: Double zinc ribbon
Probab=23.56 E-value=45 Score=19.02 Aligned_cols=29 Identities=17% Similarity=0.436 Sum_probs=19.3
Q ss_pred CCCCCccCCCCCCCCeeeeeccchhhhhcccc
Q psy6973 31 PGNLTCADCAEAGPTWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 31 ~~N~~CaDCg~~~p~waS~~~GvflC~~Csgi 62 (115)
++.++|..||.+-+ .......+|..|...
T Consensus 10 ~~~~fC~~CG~~l~---~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 10 DDAKFCPHCGTPLP---PPDQSKKICPNCGAE 38 (50)
T ss_pred ccccCChhhcCChh---hccCCCCCCcCCcCC
Confidence 45778888888776 233445677777653
No 127
>PRK04059 rpl34e 50S ribosomal protein L34e; Validated
Probab=23.13 E-value=46 Score=22.43 Aligned_cols=31 Identities=26% Similarity=0.504 Sum_probs=21.0
Q ss_pred CCCCCCccCCCCCCC-----------------Ceeeeeccchhhhhcc
Q psy6973 30 VPGNLTCADCAEAGP-----------------TWASLNLGLLLCIQCC 60 (115)
Q Consensus 30 ~~~N~~CaDCg~~~p-----------------~waS~~~GvflC~~Cs 60 (115)
.+.--.|+||+.+-. .-++-.||-.+|.+|.
T Consensus 31 ~~~~pkC~~c~~~L~Gi~~~Rp~~~~rlsK~~K~vsRaYGG~lc~~cv 78 (88)
T PRK04059 31 KPSKAKCAICGKPLNGVPRGRPVEIRKLGKTEKRPERPYGGYLCPKCL 78 (88)
T ss_pred CCCCCcCCCCCCccCCccCcchHHHHhcccccCCcccCcCceecHHHH
Confidence 445556999997521 2246678888888884
No 128
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=22.93 E-value=45 Score=22.06 Aligned_cols=29 Identities=17% Similarity=0.489 Sum_probs=21.7
Q ss_pred CCCccCCCCCCCCeeeeec--------cchhhhhccc
Q psy6973 33 NLTCADCAEAGPTWASLNL--------GLLLCIQCCG 61 (115)
Q Consensus 33 N~~CaDCg~~~p~waS~~~--------GvflC~~Csg 61 (115)
+..|..||.....|..+.. -.|+|.+|..
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~ 98 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGY 98 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCC
Confidence 6899999998887775433 3778888753
No 129
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=22.55 E-value=43 Score=17.03 Aligned_cols=10 Identities=20% Similarity=0.717 Sum_probs=5.1
Q ss_pred CCCCccCCCC
Q psy6973 32 GNLTCADCAE 41 (115)
Q Consensus 32 ~N~~CaDCg~ 41 (115)
+.++|..||+
T Consensus 15 ~~~fC~~CG~ 24 (26)
T PF13248_consen 15 DAKFCPNCGA 24 (26)
T ss_pred ccccChhhCC
Confidence 4455555554
No 130
>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=22.40 E-value=51 Score=18.67 Aligned_cols=28 Identities=21% Similarity=0.462 Sum_probs=15.8
Q ss_pred CCccCCCCCCCC---eeeeeccchhhhhccc
Q psy6973 34 LTCADCAEAGPT---WASLNLGLLLCIQCCG 61 (115)
Q Consensus 34 ~~CaDCg~~~p~---waS~~~GvflC~~Csg 61 (115)
++|.=||.+.++ -++-+-+++||.+|..
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~ 32 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECVE 32 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHHH
Confidence 467778887653 3344557999999964
No 131
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=22.20 E-value=39 Score=20.86 Aligned_cols=30 Identities=27% Similarity=0.510 Sum_probs=22.5
Q ss_pred CCCCCCccCCCCCCCCeeeeeccchhhhhccc
Q psy6973 30 VPGNLTCADCAEAGPTWASLNLGLLLCIQCCG 61 (115)
Q Consensus 30 ~~~N~~CaDCg~~~p~waS~~~GvflC~~Csg 61 (115)
.+|.+.|.-||.+.. .--.||..+|..|--
T Consensus 13 GkGsr~C~vCg~~~g--liRkygL~~CRqCFR 42 (54)
T PTZ00218 13 GKGSRQCRVCSNRHG--LIRKYGLNVCRQCFR 42 (54)
T ss_pred CCCCCeeecCCCcch--hhhhcCcchhhHHHH
Confidence 467899999998642 335788899998854
No 132
>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=21.99 E-value=44 Score=23.02 Aligned_cols=30 Identities=30% Similarity=0.706 Sum_probs=19.2
Q ss_pred CCCCCCccCCCCCCCCeeeeeccchhhhhccccc
Q psy6973 30 VPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVH 63 (115)
Q Consensus 30 ~~~N~~CaDCg~~~p~waS~~~GvflC~~CsgiH 63 (115)
.|.--.|.+||...+ +..-.+.|..|.+..
T Consensus 67 ~p~~~~C~~Cg~~~~----~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 67 EPVECECEDCSEEVS----PEIDLYRCPKCHGIM 96 (115)
T ss_pred eCcEEEcccCCCEEe----cCCcCccCcCCcCCC
Confidence 355678999994322 222257899998753
No 133
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=21.86 E-value=87 Score=22.40 Aligned_cols=43 Identities=14% Similarity=0.275 Sum_probs=28.5
Q ss_pred hHHHHHHHHHHhcCCCCCCccCCCCCCCCeeeeecc-chhhhhcccc
Q psy6973 17 SVETASLQSIRSRVPGNLTCADCAEAGPTWASLNLG-LLLCIQCCGV 62 (115)
Q Consensus 17 ~~~~~~l~~l~~~~~~N~~CaDCg~~~p~waS~~~G-vflC~~Csgi 62 (115)
..-++.|+...+ .--.|-.|+.|+..-..-+-- ...|..|++.
T Consensus 84 ~~i~~~L~~yI~---~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 84 FLLNERIEDYVR---KYVICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred HHHHHHHHHHHh---heEECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 334455555554 467899999999887642222 3579988764
No 134
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=21.70 E-value=65 Score=16.09 Aligned_cols=11 Identities=18% Similarity=0.579 Sum_probs=6.8
Q ss_pred CccCCCCCCCC
Q psy6973 35 TCADCAEAGPT 45 (115)
Q Consensus 35 ~CaDCg~~~p~ 45 (115)
+|..||+..++
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 36667776654
No 135
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=21.21 E-value=49 Score=19.73 Aligned_cols=26 Identities=23% Similarity=0.543 Sum_probs=17.4
Q ss_pred CCCCccCCCCCCCCeeeeeccchhhhhcc
Q psy6973 32 GNLTCADCAEAGPTWASLNLGLLLCIQCC 60 (115)
Q Consensus 32 ~N~~CaDCg~~~p~waS~~~GvflC~~Cs 60 (115)
-.+.|..||+. ......+-+.|..|.
T Consensus 19 ~~~fCP~Cg~~---~m~~~~~r~~C~~Cg 44 (50)
T PRK00432 19 KNKFCPRCGSG---FMAEHLDRWHCGKCG 44 (50)
T ss_pred ccCcCcCCCcc---hheccCCcEECCCcC
Confidence 36689999873 223344778888884
No 136
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.85 E-value=38 Score=23.48 Aligned_cols=47 Identities=19% Similarity=0.402 Sum_probs=26.5
Q ss_pred cCCChHHHHHHHHHHhc-------------CCCCCCccCCCCCCCCeeeeeccchhhhhcccc
Q psy6973 13 RLQSSVETASLQSIRSR-------------VPGNLTCADCAEAGPTWASLNLGLLLCIQCCGV 62 (115)
Q Consensus 13 ~~~~~~~~~~l~~l~~~-------------~~~N~~CaDCg~~~p~waS~~~GvflC~~Csgi 62 (115)
..+|+.-+-.|..+..- .|.--.|.+||...+ ...+..+.|..|.+.
T Consensus 38 ~V~pe~L~faf~~~~~~T~~~ega~L~Ie~vp~~~~C~~Cg~~~~---~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 38 GMDKSLFVSAFETFREESLVCKDAILDIVDEKVELECKDCSHVFK---PNALDYGVCEKCHSK 97 (117)
T ss_pred CcCHHHHHHHHHHHhcCCcccCCCEEEEEecCCEEEhhhCCCccc---cCCccCCcCcCCCCC
Confidence 34455555555555441 233457999994432 223344569999874
No 137
>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=20.84 E-value=32 Score=21.16 Aligned_cols=29 Identities=21% Similarity=0.504 Sum_probs=24.8
Q ss_pred CCccCCCCCCCCeee-eeccchhhhhcccc
Q psy6973 34 LTCADCAEAGPTWAS-LNLGLLLCIQCCGV 62 (115)
Q Consensus 34 ~~CaDCg~~~p~waS-~~~GvflC~~Csgi 62 (115)
..|.-|.-|...|+- ..|+-.+|..|...
T Consensus 4 q~CyLCdlPr~PWami~df~EpVCRgCvNy 33 (54)
T PF11261_consen 4 QQCYLCDLPRMPWAMIWDFSEPVCRGCVNY 33 (54)
T ss_pred eeEEeccCCCCchHHHhhccchhhhhhcCc
Confidence 469999999999996 67899999999764
Done!