Query psy8832
Match_columns 144
No_of_seqs 151 out of 802
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 20:19:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8832.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8832hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00202 ZnF_GATA Zinc finger D 99.7 5E-17 1.1E-21 102.8 3.1 43 97-139 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.6 1.8E-16 4E-21 99.5 3.3 47 95-141 3-51 (52)
3 PF00320 GATA: GATA zinc finge 99.5 4E-15 8.6E-20 86.8 1.5 35 98-132 1-36 (36)
4 cd00202 ZnF_GATA Zinc finger D 99.5 3.7E-15 8.1E-20 94.3 1.4 43 39-81 1-44 (54)
5 smart00401 ZnF_GATA zinc finge 99.5 1E-14 2.2E-19 91.6 2.6 45 36-80 2-48 (52)
6 PF00320 GATA: GATA zinc finge 99.4 2.8E-14 6.1E-19 83.2 -0.2 34 40-73 1-35 (36)
7 KOG1601|consensus 99.2 1.1E-11 2.4E-16 96.6 5.8 100 39-142 144-247 (340)
8 COG5641 GAT1 GATA Zn-finger-co 99.2 1.8E-11 4E-16 106.7 3.5 104 37-140 158-344 (498)
9 COG5641 GAT1 GATA Zn-finger-co 98.8 9.1E-10 2E-14 96.2 1.1 46 95-140 158-209 (498)
10 KOG1601|consensus 98.4 2.5E-07 5.4E-12 72.1 2.8 42 37-78 199-241 (340)
11 PF08271 TF_Zn_Ribbon: TFIIB z 89.9 0.21 4.6E-06 29.5 1.6 29 39-69 2-30 (43)
12 PF06677 Auto_anti-p27: Sjogre 88.5 0.35 7.6E-06 28.7 1.8 26 36-65 16-41 (41)
13 KOG3554|consensus 87.7 0.77 1.7E-05 40.8 4.1 47 95-141 386-436 (693)
14 PRK14559 putative protein seri 87.2 0.56 1.2E-05 43.0 3.1 23 38-67 2-24 (645)
15 TIGR01384 TFS_arch transcripti 86.6 0.56 1.2E-05 32.5 2.2 84 39-127 2-101 (104)
16 PF12773 DZR: Double zinc ribb 81.8 1.6 3.4E-05 26.1 2.5 22 95-123 29-50 (50)
17 KOG3554|consensus 81.1 1.1 2.3E-05 39.9 2.1 38 35-72 384-424 (693)
18 PRK12286 rpmF 50S ribosomal pr 81.1 0.87 1.9E-05 28.9 1.2 26 36-69 26-51 (57)
19 COG1645 Uncharacterized Zn-fin 79.1 0.97 2.1E-05 33.4 1.0 28 35-67 26-53 (131)
20 PRK03988 translation initiatio 76.3 1.3 2.8E-05 32.9 1.0 31 37-67 102-132 (138)
21 PF13248 zf-ribbon_3: zinc-rib 76.2 1.5 3.2E-05 23.1 1.0 22 38-66 3-24 (26)
22 PF11781 RRN7: RNA polymerase 76.0 1.5 3.2E-05 25.2 1.0 24 39-66 10-33 (36)
23 PF01783 Ribosomal_L32p: Ribos 75.9 1.5 3.3E-05 27.4 1.1 25 36-68 25-49 (56)
24 TIGR00311 aIF-2beta translatio 75.0 1.5 3.3E-05 32.3 1.1 30 38-67 98-127 (133)
25 smart00653 eIF2B_5 domain pres 74.9 1.5 3.3E-05 31.3 1.1 29 38-66 81-109 (110)
26 PRK14892 putative transcriptio 73.5 1.9 4E-05 30.4 1.2 36 35-70 19-54 (99)
27 PRK00420 hypothetical protein; 72.5 2.6 5.7E-05 30.3 1.8 31 36-70 22-52 (112)
28 TIGR01031 rpmF_bact ribosomal 71.2 2.2 4.8E-05 26.8 1.0 26 36-69 25-50 (55)
29 smart00105 ArfGap Putative GTP 70.6 3.5 7.6E-05 29.1 2.1 42 95-137 3-48 (112)
30 PRK03564 formate dehydrogenase 70.4 3.1 6.7E-05 34.9 2.0 71 36-129 186-265 (309)
31 TIGR01562 FdhE formate dehydro 68.4 3.9 8.4E-05 34.3 2.2 70 37-129 184-265 (305)
32 PRK03988 translation initiatio 68.1 1.8 3.9E-05 32.1 0.2 29 96-124 103-131 (138)
33 KOG2907|consensus 67.3 2.4 5.2E-05 30.6 0.6 88 36-126 6-112 (116)
34 PF01412 ArfGap: Putative GTPa 66.3 6.5 0.00014 27.9 2.8 37 93-130 11-47 (116)
35 PRK12336 translation initiatio 66.3 2.8 6.1E-05 32.8 0.9 31 38-68 99-129 (201)
36 smart00653 eIF2B_5 domain pres 66.1 2.2 4.7E-05 30.5 0.2 29 96-124 81-109 (110)
37 PF01873 eIF-5_eIF-2B: Domain 66.0 3.5 7.6E-05 30.1 1.3 29 38-66 94-122 (125)
38 PLN02400 cellulose synthase 64.8 6.8 0.00015 38.1 3.3 28 35-66 34-63 (1085)
39 smart00105 ArfGap Putative GTP 64.5 3.5 7.6E-05 29.1 1.1 37 37-74 3-39 (112)
40 KOG1598|consensus 63.7 4.3 9.2E-05 36.4 1.7 29 38-68 1-29 (521)
41 TIGR00311 aIF-2beta translatio 63.7 2.5 5.5E-05 31.2 0.2 29 96-124 98-126 (133)
42 smart00778 Prim_Zn_Ribbon Zinc 63.6 5.4 0.00012 23.1 1.6 28 39-66 5-33 (37)
43 COG5347 GTPase-activating prot 62.6 5.6 0.00012 33.5 2.1 39 34-73 17-55 (319)
44 PF01412 ArfGap: Putative GTPa 62.5 4.1 8.9E-05 28.9 1.1 38 35-73 11-48 (116)
45 PRK00423 tfb transcription ini 62.3 6.1 0.00013 32.8 2.3 30 36-67 10-39 (310)
46 PF14803 Nudix_N_2: Nudix N-te 62.1 3.4 7.3E-05 23.5 0.5 28 97-124 2-30 (34)
47 PF06689 zf-C4_ClpX: ClpX C4-t 60.8 2.3 5E-05 24.9 -0.4 29 38-66 2-32 (41)
48 PF12760 Zn_Tnp_IS1595: Transp 58.9 9.6 0.00021 22.6 2.2 26 38-65 19-44 (46)
49 PF01873 eIF-5_eIF-2B: Domain 58.1 4.8 0.0001 29.3 0.9 28 97-124 95-122 (125)
50 smart00659 RPOLCX RNA polymera 56.9 5.2 0.00011 23.9 0.7 40 97-142 4-43 (44)
51 PF07282 OrfB_Zn_ribbon: Putat 56.7 8.6 0.00019 24.3 1.8 29 36-67 27-55 (69)
52 PF04216 FdhE: Protein involve 54.7 2.2 4.8E-05 34.9 -1.6 71 37-130 172-252 (290)
53 PHA00626 hypothetical protein 54.0 9.9 0.00021 24.2 1.7 32 39-70 2-35 (59)
54 PRK01110 rpmF 50S ribosomal pr 53.0 6.6 0.00014 25.0 0.8 26 36-70 26-51 (60)
55 PF09723 Zn-ribbon_8: Zinc rib 52.9 7.4 0.00016 22.7 0.9 7 97-103 28-34 (42)
56 COG1594 RPB9 DNA-directed RNA 52.7 11 0.00024 26.9 2.0 89 37-127 2-111 (113)
57 PF09526 DUF2387: Probable met 52.6 9.9 0.00022 25.1 1.6 37 37-73 8-45 (71)
58 PF02318 FYVE_2: FYVE-type zin 52.2 8.9 0.00019 27.3 1.4 50 36-124 53-102 (118)
59 PRK12336 translation initiatio 51.7 5.1 0.00011 31.4 0.1 29 96-124 99-127 (201)
60 COG3529 Predicted nucleic-acid 48.6 7.1 0.00015 25.3 0.4 34 94-127 9-43 (66)
61 PF13240 zinc_ribbon_2: zinc-r 48.5 9.3 0.0002 19.6 0.8 7 59-65 14-20 (23)
62 COG1405 SUA7 Transcription ini 48.0 12 0.00026 31.0 1.8 29 38-68 2-30 (285)
63 KOG3740|consensus 47.8 7.2 0.00016 35.8 0.4 30 95-124 462-495 (706)
64 TIGR02443 conserved hypothetic 46.9 13 0.00027 23.9 1.3 33 37-69 9-42 (59)
65 PF01363 FYVE: FYVE zinc finge 45.6 11 0.00023 23.9 0.9 17 34-50 6-22 (69)
66 COG0333 RpmF Ribosomal protein 45.3 12 0.00027 23.7 1.1 26 36-69 26-51 (57)
67 KOG3740|consensus 44.8 7.6 0.00016 35.7 0.1 36 35-70 460-499 (706)
68 PLN03114 ADP-ribosylation fact 44.5 15 0.00033 31.7 1.8 44 93-137 20-67 (395)
69 COG5347 GTPase-activating prot 44.5 13 0.00028 31.4 1.4 37 93-130 18-54 (319)
70 smart00661 RPOL9 RNA polymeras 44.1 17 0.00036 21.6 1.5 30 39-70 2-32 (52)
71 PF09538 FYDLN_acid: Protein o 42.8 19 0.00042 25.6 1.9 32 36-71 8-39 (108)
72 PF07754 DUF1610: Domain of un 41.8 19 0.00042 18.9 1.4 23 40-65 1-23 (24)
73 TIGR02605 CxxC_CxxC_SSSS putat 41.5 16 0.00035 21.8 1.2 27 39-66 7-34 (52)
74 COG4260 Membrane protease subu 41.4 14 0.00031 31.0 1.3 47 15-66 295-342 (345)
75 PF09779 Ima1_N: Ima1 N-termin 41.1 45 0.00097 24.3 3.7 37 39-76 2-40 (131)
76 PLN02436 cellulose synthase A 40.8 27 0.00059 34.1 3.1 28 35-66 34-63 (1094)
77 PF01286 XPA_N: XPA protein N- 40.0 11 0.00024 21.4 0.3 28 37-64 3-30 (34)
78 smart00440 ZnF_C2C2 C2C2 Zinc 39.8 9.8 0.00021 22.1 0.0 29 97-125 2-37 (40)
79 PRK08351 DNA-directed RNA poly 38.9 19 0.00041 23.2 1.3 14 39-52 17-31 (61)
80 PF01096 TFIIS_C: Transcriptio 38.7 17 0.00037 20.9 1.0 28 97-124 2-36 (39)
81 cd07172 NR_DBD_GR_PR DNA-bindi 38.1 22 0.00048 23.6 1.5 31 96-130 3-33 (78)
82 PRK00432 30S ribosomal protein 38.0 21 0.00045 21.8 1.3 27 36-66 19-45 (50)
83 PF08273 Prim_Zn_Ribbon: Zinc- 37.4 16 0.00034 21.5 0.6 26 39-64 5-32 (40)
84 PF03604 DNA_RNApol_7kD: DNA d 37.2 27 0.00058 19.5 1.5 24 39-66 2-25 (32)
85 PLN03114 ADP-ribosylation fact 37.0 24 0.00052 30.5 1.9 39 35-74 20-58 (395)
86 smart00834 CxxC_CXXC_SSSS Puta 36.7 19 0.00042 20.1 1.0 28 97-124 7-34 (41)
87 TIGR03573 WbuX N-acetyl sugar 36.5 28 0.00061 29.1 2.3 31 38-70 2-33 (343)
88 PLN02915 cellulose synthase A 36.3 28 0.00061 33.9 2.5 28 35-66 13-42 (1044)
89 KOG0703|consensus 35.3 23 0.00051 29.5 1.6 34 35-69 23-56 (287)
90 KOG0706|consensus 35.3 23 0.00049 31.3 1.6 42 33-75 19-60 (454)
91 PF04981 NMD3: NMD3 family ; 35.2 33 0.00072 27.2 2.4 52 40-112 1-53 (236)
92 cd07168 NR_DBD_DHR4_like DNA-b 34.6 30 0.00065 23.6 1.8 33 94-130 5-37 (90)
93 KOG0957|consensus 34.5 36 0.00079 30.8 2.7 59 34-105 541-599 (707)
94 COG1405 SUA7 Transcription ini 34.4 18 0.00038 30.0 0.7 11 114-124 18-28 (285)
95 PRK00398 rpoP DNA-directed RNA 34.3 19 0.00042 21.1 0.7 27 38-67 4-30 (46)
96 PLN02638 cellulose synthase A 34.2 29 0.00062 33.9 2.2 29 34-66 14-44 (1079)
97 PRK14559 putative protein seri 33.4 44 0.00095 30.9 3.2 46 33-110 11-56 (645)
98 PF09297 zf-NADH-PPase: NADH p 33.1 32 0.0007 18.6 1.5 27 37-67 3-30 (32)
99 cd07170 NR_DBD_ERR DNA-binding 32.9 30 0.00065 24.0 1.6 31 96-130 5-35 (97)
100 PRK06393 rpoE DNA-directed RNA 32.9 28 0.0006 22.6 1.3 16 37-52 17-33 (64)
101 cd07171 NR_DBD_ER DNA-binding 32.7 33 0.00071 23.0 1.7 31 96-130 4-34 (82)
102 PF08792 A2L_zn_ribbon: A2L zi 32.6 44 0.00096 18.6 2.0 29 37-68 3-31 (33)
103 PRK00085 recO DNA repair prote 31.6 34 0.00074 26.7 1.9 30 36-65 148-177 (247)
104 cd07173 NR_DBD_AR DNA-binding 31.1 35 0.00076 22.9 1.7 31 96-130 4-34 (82)
105 COG4888 Uncharacterized Zn rib 30.6 13 0.00027 26.4 -0.6 31 97-127 24-57 (104)
106 KOG1597|consensus 30.5 40 0.00087 28.3 2.2 29 39-67 2-30 (308)
107 COG1996 RPC10 DNA-directed RNA 30.3 21 0.00046 22.0 0.4 41 97-142 8-48 (49)
108 PF10571 UPF0547: Uncharacteri 30.1 36 0.00077 18.0 1.2 7 60-66 16-22 (26)
109 PF00105 zf-C4: Zinc finger, C 29.4 35 0.00076 21.7 1.4 29 97-129 2-30 (70)
110 COG1997 RPL43A Ribosomal prote 28.3 39 0.00085 23.3 1.5 33 36-71 34-66 (89)
111 PRK14714 DNA polymerase II lar 28.1 49 0.0011 33.0 2.7 22 37-67 667-688 (1337)
112 PRK14890 putative Zn-ribbon RN 27.6 57 0.0012 20.9 2.1 27 37-66 7-33 (59)
113 cd07162 NR_DBD_PXR DNA-binding 26.8 44 0.00096 22.5 1.6 29 98-130 2-30 (87)
114 COG1499 NMD3 NMD protein affec 26.7 39 0.00084 28.9 1.6 60 35-115 4-64 (355)
115 cd06955 NR_DBD_VDR DNA-binding 26.7 24 0.00052 25.0 0.3 33 94-130 5-37 (107)
116 COG2816 NPY1 NTP pyrophosphohy 26.6 40 0.00087 28.0 1.6 28 36-67 110-138 (279)
117 PF04161 Arv1: Arv1-like famil 26.2 33 0.00072 26.8 1.0 30 39-68 2-34 (208)
118 PF04810 zf-Sec23_Sec24: Sec23 26.1 33 0.00072 19.7 0.8 31 37-67 2-33 (40)
119 cd06963 NR_DBD_GR_like The DNA 25.6 42 0.00092 21.8 1.3 16 115-130 14-29 (73)
120 KOG1729|consensus 25.5 61 0.0013 27.0 2.5 22 32-53 163-185 (288)
121 cd07155 NR_DBD_ER_like DNA-bin 25.3 44 0.00094 21.8 1.3 15 115-129 14-28 (75)
122 PLN02189 cellulose synthase 24.6 53 0.0011 32.1 2.1 29 34-66 31-61 (1040)
123 COG0675 Transposase and inacti 24.6 45 0.00097 26.5 1.5 26 34-67 306-331 (364)
124 KOG1194|consensus 24.2 14 0.0003 32.9 -1.6 42 97-138 264-305 (534)
125 PF10058 DUF2296: Predicted in 24.2 45 0.00097 20.7 1.1 34 33-66 18-52 (54)
126 cd07158 NR_DBD_Ppar_like The D 23.9 48 0.001 21.4 1.3 16 115-130 14-29 (73)
127 PLN03119 putative ADP-ribosyla 23.8 45 0.00098 30.6 1.5 33 36-69 22-54 (648)
128 cd06966 NR_DBD_CAR DNA-binding 23.8 51 0.0011 22.6 1.5 29 39-71 2-30 (94)
129 COG2331 Uncharacterized protei 23.8 34 0.00074 23.2 0.5 32 97-128 14-45 (82)
130 cd07179 2DBD_NR_DBD2 The secon 23.5 54 0.0012 21.3 1.5 16 115-130 14-29 (74)
131 TIGR01385 TFSII transcription 23.3 72 0.0016 26.6 2.5 36 34-69 255-297 (299)
132 KOG2879|consensus 23.3 94 0.002 26.0 3.1 57 33-110 235-291 (298)
133 cd07169 NR_DBD_GCNF_like DNA-b 23.1 65 0.0014 21.9 1.9 31 96-130 7-37 (90)
134 cd06968 NR_DBD_ROR DNA-binding 23.0 66 0.0014 22.1 1.9 31 96-130 6-36 (95)
135 PF08274 PhnA_Zn_Ribbon: PhnA 22.8 30 0.00065 19.0 0.1 24 96-123 3-26 (30)
136 PF00130 C1_1: Phorbol esters/ 22.5 46 0.001 19.6 0.9 30 35-68 9-38 (53)
137 COG2191 Formylmethanofuran deh 22.4 52 0.0011 26.1 1.4 31 36-66 171-201 (206)
138 cd06970 NR_DBD_PNR DNA-binding 21.9 75 0.0016 21.7 2.0 32 36-71 5-36 (92)
139 PF10005 DUF2248: Uncharacteri 21.7 1.2E+02 0.0025 26.1 3.4 31 93-124 51-82 (343)
140 PLN03119 putative ADP-ribosyla 21.6 49 0.0011 30.4 1.3 36 93-129 21-56 (648)
141 PF14471 DUF4428: Domain of un 21.0 59 0.0013 19.9 1.2 27 98-125 2-29 (51)
142 PRK13130 H/ACA RNA-protein com 20.9 48 0.001 20.9 0.8 24 35-67 3-26 (56)
143 PLN03131 hypothetical protein; 20.8 57 0.0012 30.2 1.5 33 36-69 22-54 (705)
144 cd06967 NR_DBD_TR2_like DNA-bi 20.7 70 0.0015 21.6 1.6 31 37-71 3-33 (87)
145 COG3952 Predicted membrane pro 20.5 26 0.00055 25.2 -0.6 21 108-129 76-96 (113)
146 PHA02942 putative transposase; 20.3 79 0.0017 27.1 2.2 28 36-67 324-351 (383)
No 1
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.66 E-value=5e-17 Score=102.84 Aligned_cols=43 Identities=51% Similarity=1.018 Sum_probs=40.5
Q ss_pred ccccCCcccccccccCCCC-CcccchhHHHHHhhCCCCcccccc
Q psy8832 97 SCANCSTTCTTLWRRNNNG-EPVCNACGLYFKLHNVFTILFYNI 139 (144)
Q Consensus 97 ~C~nC~t~~t~~WR~~~~g-~~lCnaCglyy~~~~~~Rp~~l~~ 139 (144)
+|+||++++||+||+++++ ..|||||||||++++..||++++.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRK 44 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCc
Confidence 5999999999999999954 899999999999999999999987
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.63 E-value=1.8e-16 Score=99.51 Aligned_cols=47 Identities=49% Similarity=0.931 Sum_probs=43.4
Q ss_pred CcccccCCcccccccccCCCCC-cccchhHHHHHhhCCC-Ccccccccc
Q psy8832 95 GVSCANCSTTCTTLWRRNNNGE-PVCNACGLYFKLHNVF-TILFYNITK 141 (144)
Q Consensus 95 ~~~C~nC~t~~t~~WR~~~~g~-~lCnaCglyy~~~~~~-Rp~~l~~~~ 141 (144)
+..|+||++++||+||+++.|. .|||||||||++++.. ||+++.++.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~~~~ 51 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLKKDV 51 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCCCCcccccccC
Confidence 4689999999999999999995 9999999999999988 999998864
No 3
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.51 E-value=4e-15 Score=86.77 Aligned_cols=35 Identities=54% Similarity=1.127 Sum_probs=28.2
Q ss_pred cccCCcccccccccCCCCCc-ccchhHHHHHhhCCC
Q psy8832 98 CANCSTTCTTLWRRNNNGEP-VCNACGLYFKLHNVF 132 (144)
Q Consensus 98 C~nC~t~~t~~WR~~~~g~~-lCnaCglyy~~~~~~ 132 (144)
|+||++++||+||++++|.. |||+||+||++|+++
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~~ 36 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGKM 36 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS-
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCCC
Confidence 89999999999999999955 999999999999863
No 4
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.51 E-value=3.7e-15 Score=94.27 Aligned_cols=43 Identities=51% Similarity=1.104 Sum_probs=38.9
Q ss_pred ccccCCCCCCCeeeeCCCC-CcccccccccccccCCCCCCcccc
Q psy8832 39 ECVNCAANSTPLWRRDGTG-HHLCNACGLYNRINGVNRPPVRTN 81 (144)
Q Consensus 39 ~C~~C~t~~tp~wrr~~~g-~~lCnaCgly~r~~g~~RP~~k~k 81 (144)
+|+||++++||+||++++| ..||||||||+++++..+|.....
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRK 44 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCc
Confidence 5999999999999999955 789999999999999999987654
No 5
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.50 E-value=1e-14 Score=91.57 Aligned_cols=45 Identities=47% Similarity=0.969 Sum_probs=39.8
Q ss_pred CCcccccCCCCCCCeeeeCCCCC-cccccccccccccCCC-CCCccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGH-HLCNACGLYNRINGVN-RPPVRT 80 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~-~lCnaCgly~r~~g~~-RP~~k~ 80 (144)
....|+||++++||+||+++.|. .||||||||+++++.. +|....
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~ 48 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLK 48 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCCCCccccc
Confidence 35689999999999999999996 8999999999999887 776544
No 6
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.41 E-value=2.8e-14 Score=83.17 Aligned_cols=34 Identities=53% Similarity=1.189 Sum_probs=27.7
Q ss_pred cccCCCCCCCeeeeCCCCCc-ccccccccccccCC
Q psy8832 40 CVNCAANSTPLWRRDGTGHH-LCNACGLYNRINGV 73 (144)
Q Consensus 40 C~~C~t~~tp~wrr~~~g~~-lCnaCgly~r~~g~ 73 (144)
|++|++++||+||++++|.. ||||||+|+++++.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 89999999999999999976 99999999998764
No 7
>KOG1601|consensus
Probab=99.24 E-value=1.1e-11 Score=96.65 Aligned_cols=100 Identities=33% Similarity=0.514 Sum_probs=75.5
Q ss_pred ccccCCCCCCCeeeeCCCCCcccccccccccccCCCCC--CccccchhhhhhcCCCCC-CcccccCCcccccccccCCCC
Q psy8832 39 ECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVNRP--PVRTNQKKALQQTGNKRS-GVSCANCSTTCTTLWRRNNNG 115 (144)
Q Consensus 39 ~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~g~~RP--~~k~kkkka~~~s~~k~~-~~~C~nC~t~~t~~WR~~~~g 115 (144)
.|.+++...++.|+.+..+..++.+++++.......++ .....++. ...... ...|++|+++.||+||+++.|
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~c~~~~~~~t~~~r~~~~g 219 (340)
T KOG1601|consen 144 ESVSSLLFPTPLQRRDSSGHYNSINKELKKKSNGESSSDLESKPKKSS----SASSEQNLRQCSNCGTTKTPLWRRGPEG 219 (340)
T ss_pred ccccccccccceeccCCCCccccccccccccccccccCCccccchhhh----hccccccCcccCCCCCCCCcceecCCCC
Confidence 89999999999999887777788887755555544442 22222111 111111 479999999999999999999
Q ss_pred -CcccchhHHHHHhhCCCCccccccccc
Q psy8832 116 -EPVCNACGLYFKLHNVFTILFYNITKA 142 (144)
Q Consensus 116 -~~lCnaCglyy~~~~~~Rp~~l~~~~~ 142 (144)
..+|||||+||+++++.|++.+++..+
T Consensus 220 ~~~~cnacgl~~k~~~~~r~~~~~~~~~ 247 (340)
T KOG1601|consen 220 PKSLCNACGLRYKKGGVRRPLPEKRPAS 247 (340)
T ss_pred CccccccchhhhhhcCccccccccCccc
Confidence 999999999999999999999887654
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=99.16 E-value=1.8e-11 Score=106.73 Aligned_cols=104 Identities=35% Similarity=0.591 Sum_probs=76.7
Q ss_pred CcccccCCCCCCCeeeeCCC-----CCcccccccccccccCCCC-CCccccch----h----------hhh-----h---
Q psy8832 37 IKECVNCAANSTPLWRRDGT-----GHHLCNACGLYNRINGVNR-PPVRTNQK----K----------ALQ-----Q--- 88 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr~~~-----g~~lCnaCgly~r~~g~~R-P~~k~kkk----k----------a~~-----~--- 88 (144)
..+|.||.|+.||+|||+.. |.++|||||||++.||..| |.....+- . ..+ .
T Consensus 158 ~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks~~~ks~~~~~~~~~n~~~~~~~n~~S~~~ 237 (498)
T COG5641 158 PHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSDSIKSRSSRSSHNNNDSNGENANTESIGN 237 (498)
T ss_pred cchhccccccCCccccccccccccCCccccccccccccccCCcCCCcccccccccccccccccccccccccccccccccc
Confidence 44999999999999999998 8899999999999999999 75422110 0 000 0
Q ss_pred -------------cC----------------------------------------CCCCCcccccCCc-ccccccccCCC
Q psy8832 89 -------------TG----------------------------------------NKRSGVSCANCST-TCTTLWRRNNN 114 (144)
Q Consensus 89 -------------s~----------------------------------------~k~~~~~C~nC~t-~~t~~WR~~~~ 114 (144)
.. .-.....+++|.+ +.||+||+...
T Consensus 238 ~~~~~~~~s~~~~~~~~~~~~~~~~~~~~s~~~k~~~le~l~gs~~~~~~~tp~~~~ps~~~~s~~~~~~~tp~~~r~~~ 317 (498)
T COG5641 238 SSASKLTKSWEERPQGRQLLSDAGSLSPRSNNPKSPLLEGLMGSTSLQPVSTPKLVLPSDKKRSTLTTSTATPLWRRTSD 317 (498)
T ss_pred cccccccchhhhccccccccccccccccccCCCcchhhhhcccCccccccCCccccchhhcCcccccccccCcccccccc
Confidence 00 0001236777766 67888877654
Q ss_pred -CCcccchhHHHHHhhCCCCccccccc
Q psy8832 115 -GEPVCNACGLYFKLHNVFTILFYNIT 140 (144)
Q Consensus 115 -g~~lCnaCglyy~~~~~~Rp~~l~~~ 140 (144)
..+.||+|+++-+.++++||+..|-+
T Consensus 318 ~~s~~~n~~~~~~~~~~~~~p~~pk~d 344 (498)
T COG5641 318 KSSFSCNASGSALKPPGSKRPLLPKPD 344 (498)
T ss_pred cccccccccccccCCcccccccCCCCC
Confidence 48999999999999999999987644
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.82 E-value=9.1e-10 Score=96.21 Aligned_cols=46 Identities=46% Similarity=0.892 Sum_probs=43.0
Q ss_pred CcccccCCcccccccccCCC-----CCcccchhHHHHHhhCCCC-ccccccc
Q psy8832 95 GVSCANCSTTCTTLWRRNNN-----GEPVCNACGLYFKLHNVFT-ILFYNIT 140 (144)
Q Consensus 95 ~~~C~nC~t~~t~~WR~~~~-----g~~lCnaCglyy~~~~~~R-p~~l~~~ 140 (144)
+.+|.||.++.||+|||... |..+||||||||+.||.+| |++||.+
T Consensus 158 ~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks~ 209 (498)
T COG5641 158 PHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSD 209 (498)
T ss_pred cchhccccccCCccccccccccccCCccccccccccccccCCcCCCcccccc
Confidence 34999999999999999999 8999999999999999999 9999864
No 10
>KOG1601|consensus
Probab=98.35 E-value=2.5e-07 Score=72.07 Aligned_cols=42 Identities=50% Similarity=1.093 Sum_probs=37.2
Q ss_pred CcccccCCCCCCCeeeeCCCC-CcccccccccccccCCCCCCc
Q psy8832 37 IKECVNCAANSTPLWRRDGTG-HHLCNACGLYNRINGVNRPPV 78 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr~~~g-~~lCnaCgly~r~~g~~RP~~ 78 (144)
...|++|+++.||+||+++.| ..+|||||+|+++++..++..
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~ 241 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLP 241 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCcccccc
Confidence 479999999999999999999 899999999999998555543
No 11
>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=89.90 E-value=0.21 Score=29.47 Aligned_cols=29 Identities=28% Similarity=0.683 Sum_probs=20.8
Q ss_pred ccccCCCCCCCeeeeCCCCCccccccccccc
Q psy8832 39 ECVNCAANSTPLWRRDGTGHHLCNACGLYNR 69 (144)
Q Consensus 39 ~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r 69 (144)
.|.+||++. +--....|..+|..||+-..
T Consensus 2 ~Cp~Cg~~~--~~~D~~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCPNCGSKE--IVFDPERGELVCPNCGLVLE 30 (43)
T ss_dssp SBTTTSSSE--EEEETTTTEEEETTT-BBEE
T ss_pred CCcCCcCCc--eEEcCCCCeEECCCCCCEee
Confidence 699999876 33335678899999998543
No 12
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=88.52 E-value=0.35 Score=28.73 Aligned_cols=26 Identities=42% Similarity=0.930 Sum_probs=21.2
Q ss_pred CCcccccCCCCCCCeeeeCCCCCccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACG 65 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCg 65 (144)
....|..|| +|+.| +.+|..+|-+|+
T Consensus 16 L~~~Cp~C~---~PL~~-~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 16 LDEHCPDCG---TPLMR-DKDGKIYCVSCG 41 (41)
T ss_pred hcCccCCCC---CeeEE-ecCCCEECCCCC
Confidence 455799997 99999 667888999985
No 13
>KOG3554|consensus
Probab=87.72 E-value=0.77 Score=40.77 Aligned_cols=47 Identities=21% Similarity=0.423 Sum_probs=36.0
Q ss_pred CcccccCCccccccccc-CCCC--CcccchhHHHHHhhC-CCCcccccccc
Q psy8832 95 GVSCANCSTTCTTLWRR-NNNG--EPVCNACGLYFKLHN-VFTILFYNITK 141 (144)
Q Consensus 95 ~~~C~nC~t~~t~~WR~-~~~g--~~lCnaCglyy~~~~-~~Rp~~l~~~~ 141 (144)
+.-|.+|.|+.+-.|=. |+-+ -.||..|-+||++.| .+-|-.|.+.+
T Consensus 386 g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKygGLk~ptqle~~~ 436 (693)
T KOG3554|consen 386 GRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYGGLKMPTQLEGED 436 (693)
T ss_pred CCcccccccccccceeccCCCCccchhhHHHHHHHHHhcCcCCcchhcccc
Confidence 56899999999999843 3333 678999999999995 66666665544
No 14
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=87.23 E-value=0.56 Score=42.98 Aligned_cols=23 Identities=22% Similarity=0.689 Sum_probs=15.4
Q ss_pred cccccCCCCCCCeeeeCCCCCccccccccc
Q psy8832 38 KECVNCAANSTPLWRRDGTGHHLCNACGLY 67 (144)
Q Consensus 38 ~~C~~C~t~~tp~wrr~~~g~~lCnaCgly 67 (144)
..|.+||+. .++|..+|..||..
T Consensus 2 ~~Cp~Cg~~-------n~~~akFC~~CG~~ 24 (645)
T PRK14559 2 LICPQCQFE-------NPNNNRFCQKCGTS 24 (645)
T ss_pred CcCCCCCCc-------CCCCCccccccCCC
Confidence 568888865 34455688888773
No 15
>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=86.62 E-value=0.56 Score=32.51 Aligned_cols=84 Identities=21% Similarity=0.515 Sum_probs=45.2
Q ss_pred ccccCCCCCCCeeeeCCCCCcccccccccccccCC-CCC--Cccccc-hhhh----h-hcCCCCCCcccccCCccccccc
Q psy8832 39 ECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGV-NRP--PVRTNQ-KKAL----Q-QTGNKRSGVSCANCSTTCTTLW 109 (144)
Q Consensus 39 ~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~g~-~RP--~~k~kk-kka~----~-~s~~k~~~~~C~nC~t~~t~~W 109 (144)
.|.+||.--.|. .+.+.|..||..+..... ... .....+ .... + ..........|.+|+..+.-.|
T Consensus 2 fC~~Cg~~l~~~-----~~~~~C~~C~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~~~a~f~ 76 (104)
T TIGR01384 2 FCPKCGSLMTPK-----NGVYVCPSCGYEKEKKPEDDYKVTEKVKHKIKETIIIREEDSETLPTTRVECPKCGHKEAYYW 76 (104)
T ss_pred CCcccCcccccC-----CCeEECcCCCCccccccccccEEEEEeccccccceeeccccccCCCcccCCCCCCCCCeeEEE
Confidence 588998655441 356899999975543210 000 000000 0000 0 0111234678999998886655
Q ss_pred ----ccCCCC---CcccchhHHHHH
Q psy8832 110 ----RRNNNG---EPVCNACGLYFK 127 (144)
Q Consensus 110 ----R~~~~g---~~lCnaCglyy~ 127 (144)
|...++ -.+|-.|+..|+
T Consensus 77 ~~Q~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 77 LLQTRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred EeccCCCCCCcEEEEEeCCCCCeeE
Confidence 445556 344988987664
No 16
>PF12773 DZR: Double zinc ribbon
Probab=81.79 E-value=1.6 Score=26.12 Aligned_cols=22 Identities=27% Similarity=0.729 Sum_probs=11.9
Q ss_pred CcccccCCcccccccccCCCCCcccchhH
Q psy8832 95 GVSCANCSTTCTTLWRRNNNGEPVCNACG 123 (144)
Q Consensus 95 ~~~C~nC~t~~t~~WR~~~~g~~lCnaCg 123 (144)
...|.+|+... ..+..+|..||
T Consensus 29 ~~~C~~Cg~~~-------~~~~~fC~~CG 50 (50)
T PF12773_consen 29 KKICPNCGAEN-------PPNAKFCPNCG 50 (50)
T ss_pred CCCCcCCcCCC-------cCCcCccCccc
Confidence 34677777732 22344566554
No 17
>KOG3554|consensus
Probab=81.15 E-value=1.1 Score=39.89 Aligned_cols=38 Identities=24% Similarity=0.594 Sum_probs=31.3
Q ss_pred CCCcccccCCCCCCCeeee-CCCCC--cccccccccccccC
Q psy8832 35 MDIKECVNCAANSTPLWRR-DGTGH--HLCNACGLYNRING 72 (144)
Q Consensus 35 ~~~~~C~~C~t~~tp~wrr-~~~g~--~lCnaCgly~r~~g 72 (144)
...+-|.+|+|+..-.|-. |+.+. .||-.|-+||++.|
T Consensus 384 ~~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKyg 424 (693)
T KOG3554|consen 384 QDGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYG 424 (693)
T ss_pred CCCCcccccccccccceeccCCCCccchhhHHHHHHHHHhc
Confidence 3477899999999999975 66553 59999999998764
No 18
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=81.14 E-value=0.87 Score=28.87 Aligned_cols=26 Identities=38% Similarity=1.045 Sum_probs=20.6
Q ss_pred CCcccccCCCCCCCeeeeCCCCCccccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLYNR 69 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r 69 (144)
..-.|.+||...-| +.+|..||.|..
T Consensus 26 ~l~~C~~CG~~~~~--------H~vC~~CG~Y~g 51 (57)
T PRK12286 26 GLVECPNCGEPKLP--------HRVCPSCGYYKG 51 (57)
T ss_pred cceECCCCCCccCC--------eEECCCCCcCCC
Confidence 34579999977766 579999998854
No 19
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=79.08 E-value=0.97 Score=33.42 Aligned_cols=28 Identities=43% Similarity=0.962 Sum_probs=24.0
Q ss_pred CCCcccccCCCCCCCeeeeCCCCCccccccccc
Q psy8832 35 MDIKECVNCAANSTPLWRRDGTGHHLCNACGLY 67 (144)
Q Consensus 35 ~~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly 67 (144)
.....|..|| +|+.+ .+|..+|..||..
T Consensus 26 ML~~hCp~Cg---~PLF~--KdG~v~CPvC~~~ 53 (131)
T COG1645 26 MLAKHCPKCG---TPLFR--KDGEVFCPVCGYR 53 (131)
T ss_pred HHHhhCcccC---Cccee--eCCeEECCCCCce
Confidence 4567899999 89999 8888999999953
No 20
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=76.26 E-value=1.3 Score=32.95 Aligned_cols=31 Identities=26% Similarity=0.462 Sum_probs=23.3
Q ss_pred CcccccCCCCCCCeeeeCCCCCccccccccc
Q psy8832 37 IKECVNCAANSTPLWRRDGTGHHLCNACGLY 67 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly 67 (144)
--.|..|+...|-+-+.+..=...|+|||-.
T Consensus 102 yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred cEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 3579999999999876433224699999974
No 21
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=76.22 E-value=1.5 Score=23.15 Aligned_cols=22 Identities=36% Similarity=0.884 Sum_probs=14.2
Q ss_pred cccccCCCCCCCeeeeCCCCCcccccccc
Q psy8832 38 KECVNCAANSTPLWRRDGTGHHLCNACGL 66 (144)
Q Consensus 38 ~~C~~C~t~~tp~wrr~~~g~~lCnaCgl 66 (144)
+.|.+||+...+ +..+|..||.
T Consensus 3 ~~Cp~Cg~~~~~-------~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDP-------DAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCc-------ccccChhhCC
Confidence 568888874332 3457888874
No 22
>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=76.02 E-value=1.5 Score=25.22 Aligned_cols=24 Identities=29% Similarity=0.886 Sum_probs=20.0
Q ss_pred ccccCCCCCCCeeeeCCCCCcccccccc
Q psy8832 39 ECVNCAANSTPLWRRDGTGHHLCNACGL 66 (144)
Q Consensus 39 ~C~~C~t~~tp~wrr~~~g~~lCnaCgl 66 (144)
.|..|+.. |-...+|.+.|..||-
T Consensus 10 ~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCe----EeEccCCEEEhhhCce
Confidence 49999965 6678999999999984
No 23
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=75.89 E-value=1.5 Score=27.43 Aligned_cols=25 Identities=36% Similarity=1.096 Sum_probs=18.6
Q ss_pred CCcccccCCCCCCCeeeeCCCCCcccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLYN 68 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~ 68 (144)
....|.+||.-.-| +.+|.+||.|.
T Consensus 25 ~l~~c~~cg~~~~~--------H~vc~~cG~y~ 49 (56)
T PF01783_consen 25 NLVKCPNCGEPKLP--------HRVCPSCGYYK 49 (56)
T ss_dssp SEEESSSSSSEEST--------TSBCTTTBBSS
T ss_pred ceeeeccCCCEecc--------cEeeCCCCeEC
Confidence 44679999965544 57999999664
No 24
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=75.00 E-value=1.5 Score=32.35 Aligned_cols=30 Identities=23% Similarity=0.502 Sum_probs=22.7
Q ss_pred cccccCCCCCCCeeeeCCCCCccccccccc
Q psy8832 38 KECVNCAANSTPLWRRDGTGHHLCNACGLY 67 (144)
Q Consensus 38 ~~C~~C~t~~tp~wrr~~~g~~lCnaCgly 67 (144)
-.|..|+...|-+-+.+..-...|+|||-.
T Consensus 98 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred EECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 579999999999876433223589999974
No 25
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=74.94 E-value=1.5 Score=31.29 Aligned_cols=29 Identities=28% Similarity=0.557 Sum_probs=22.2
Q ss_pred cccccCCCCCCCeeeeCCCCCcccccccc
Q psy8832 38 KECVNCAANSTPLWRRDGTGHHLCNACGL 66 (144)
Q Consensus 38 ~~C~~C~t~~tp~wrr~~~g~~lCnaCgl 66 (144)
-.|..|+...|-+-+.+..-..-|+|||.
T Consensus 81 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 57999999999987763322457999995
No 26
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=73.49 E-value=1.9 Score=30.40 Aligned_cols=36 Identities=28% Similarity=0.565 Sum_probs=23.3
Q ss_pred CCCcccccCCCCCCCeeeeCCCCCcccccccccccc
Q psy8832 35 MDIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRI 70 (144)
Q Consensus 35 ~~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~ 70 (144)
.....|.+||...-+.=....-++..|..||+|+..
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 345689999943222111124557899999999765
No 27
>PRK00420 hypothetical protein; Validated
Probab=72.51 E-value=2.6 Score=30.29 Aligned_cols=31 Identities=26% Similarity=0.508 Sum_probs=24.6
Q ss_pred CCcccccCCCCCCCeeeeCCCCCcccccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRI 70 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~ 70 (144)
....|..|| +|+.+- .+|+.+|.+||-....
T Consensus 22 l~~~CP~Cg---~pLf~l-k~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 22 LSKHCPVCG---LPLFEL-KDGEVVCPVHGKVYIV 52 (112)
T ss_pred ccCCCCCCC---Ccceec-CCCceECCCCCCeeee
Confidence 456899999 788774 7788999999986543
No 28
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=71.23 E-value=2.2 Score=26.76 Aligned_cols=26 Identities=35% Similarity=0.945 Sum_probs=19.6
Q ss_pred CCcccccCCCCCCCeeeeCCCCCccccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLYNR 69 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r 69 (144)
..-.|.+||...-| +.+|..||.|..
T Consensus 25 ~l~~C~~cG~~~~~--------H~vc~~cG~Y~g 50 (55)
T TIGR01031 25 TLVVCPNCGEFKLP--------HRVCPSCGYYKG 50 (55)
T ss_pred cceECCCCCCcccC--------eeECCccCeECC
Confidence 44579999976655 579999997743
No 29
>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=70.57 E-value=3.5 Score=29.10 Aligned_cols=42 Identities=21% Similarity=0.409 Sum_probs=33.9
Q ss_pred CcccccCCcccccccccCCCCCcccchhHHHHHhhCC----CCcccc
Q psy8832 95 GVSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHNV----FTILFY 137 (144)
Q Consensus 95 ~~~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~~----~Rp~~l 137 (144)
+..|.+|+. ..|.|=..+-|-.||-.|.-.-+..|+ -|.++|
T Consensus 3 N~~CaDC~~-~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~m 48 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTL 48 (112)
T ss_pred CCcccCCCC-CCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeeccc
Confidence 468999998 558999888899999999988888774 455555
No 30
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=70.43 E-value=3.1 Score=34.92 Aligned_cols=71 Identities=23% Similarity=0.532 Sum_probs=45.5
Q ss_pred CCcccccCCCCCCCee-ee-CCCC--CcccccccccccccCCCCCCccccchhhhhhcCCCCCCcccccCCccccc-ccc
Q psy8832 36 DIKECVNCAANSTPLW-RR-DGTG--HHLCNACGLYNRINGVNRPPVRTNQKKALQQTGNKRSGVSCANCSTTCTT-LWR 110 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~w-rr-~~~g--~~lCnaCgly~r~~g~~RP~~k~kkkka~~~s~~k~~~~~C~nC~t~~t~-~WR 110 (144)
....|-.||+...--+ +. +.+| ...|.-|+--|... -..|.+|+.++.- .|-
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~-----------------------R~~C~~Cg~~~~l~y~~ 242 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVV-----------------------RVKCSNCEQSGKLHYWS 242 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCccccc-----------------------CccCCCCCCCCceeeee
Confidence 3568999998764443 32 3455 35899998865522 1279999876544 353
Q ss_pred cCCC--C--CcccchhHHHHHhh
Q psy8832 111 RNNN--G--EPVCNACGLYFKLH 129 (144)
Q Consensus 111 ~~~~--g--~~lCnaCglyy~~~ 129 (144)
-.++ + -.+|..|+-|.|.-
T Consensus 243 ~~~~~~~~r~e~C~~C~~YlK~~ 265 (309)
T PRK03564 243 LDSEQAAVKAESCGDCGTYLKIL 265 (309)
T ss_pred ecCCCcceEeeecccccccceec
Confidence 2221 2 35699999998875
No 31
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=68.41 E-value=3.9 Score=34.25 Aligned_cols=70 Identities=20% Similarity=0.432 Sum_probs=45.5
Q ss_pred CcccccCCCCCCCee-eeC--CCC--CcccccccccccccCCCCCCccccchhhhhhcCCCCCCcccccCCccccc-ccc
Q psy8832 37 IKECVNCAANSTPLW-RRD--GTG--HHLCNACGLYNRINGVNRPPVRTNQKKALQQTGNKRSGVSCANCSTTCTT-LWR 110 (144)
Q Consensus 37 ~~~C~~C~t~~tp~w-rr~--~~g--~~lCnaCgly~r~~g~~RP~~k~kkkka~~~s~~k~~~~~C~nC~t~~t~-~WR 110 (144)
.-.|-.||+...--+ +.+ .+| ...|.-|+--|... -..|.+|+.++.- .|-
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~-----------------------R~~C~~Cg~~~~l~y~~ 240 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYV-----------------------RVKCSHCEESKHLAYLS 240 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccccc-----------------------CccCCCCCCCCceeeEe
Confidence 347999998765443 332 356 35899998865522 1279999887643 354
Q ss_pred cCC----CC--CcccchhHHHHHhh
Q psy8832 111 RNN----NG--EPVCNACGLYFKLH 129 (144)
Q Consensus 111 ~~~----~g--~~lCnaCglyy~~~ 129 (144)
-.. .+ -.+|..|+-|.|.-
T Consensus 241 ~e~~~~~~~~r~e~C~~C~~YlK~~ 265 (305)
T TIGR01562 241 LEHDAEKAVLKAETCDSCQGYLKIL 265 (305)
T ss_pred ecCCCCCcceEEeeccccccchhhh
Confidence 221 22 33699999998875
No 32
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=68.12 E-value=1.8 Score=32.15 Aligned_cols=29 Identities=31% Similarity=0.600 Sum_probs=22.1
Q ss_pred cccccCCcccccccccCCCCCcccchhHH
Q psy8832 96 VSCANCSTTCTTLWRRNNNGEPVCNACGL 124 (144)
Q Consensus 96 ~~C~nC~t~~t~~WR~~~~g~~lCnaCgl 124 (144)
-.|..|+..+|-+=+.+..-...|+|||-
T Consensus 103 VlC~~C~spdT~l~k~~r~~~l~C~ACGa 131 (138)
T PRK03988 103 VICPECGSPDTKLIKEGRIWVLKCEACGA 131 (138)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCC
Confidence 37999999999997643322455999986
No 33
>KOG2907|consensus
Probab=67.35 E-value=2.4 Score=30.64 Aligned_cols=88 Identities=18% Similarity=0.394 Sum_probs=48.3
Q ss_pred CCcccccCCCCCCCeeeeCCCCCcccccccccccccCCC------------CCCccccchhhhhhcCCCCCCcccccCCc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVN------------RPPVRTNQKKALQQTGNKRSGVSCANCST 103 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~g~~------------RP~~k~kkkka~~~s~~k~~~~~C~nC~t 103 (144)
...-|+.||+ -+--.+..+..+|..|..-|...-.. .+....-+...-.......+...|..|+-
T Consensus 6 ~~~FC~~CG~---ll~~~~~~~~~~C~~Ck~~~~v~~~~~~~v~~~~~~~~~~~A~~~~ve~~~~~~ga~I~~kCpkCgh 82 (116)
T KOG2907|consen 6 DLDFCSDCGS---LLEEPSAQSTVLCIRCKIEYPVSQFSGLVVETKSLFDEFTSALAEKVENESSADGAVIKHKCPKCGH 82 (116)
T ss_pred Ccchhhhhhh---hcccccccCceEeccccccCCHHHhCCeeEEEEEeecccchhhhhhhcccccccccchhccCcccCC
Confidence 4567999994 33333444556799998755432111 11111100000000112345678999987
Q ss_pred cc----ccccccCCCCCcc---cchhHHHH
Q psy8832 104 TC----TTLWRRNNNGEPV---CNACGLYF 126 (144)
Q Consensus 104 ~~----t~~WR~~~~g~~l---CnaCglyy 126 (144)
.+ |-.-|...+|+++ |-.|+..+
T Consensus 83 e~m~Y~T~QlRSADEGQTVFYTC~kC~~k~ 112 (116)
T KOG2907|consen 83 EEMSYHTLQLRSADEGQTVFYTCPKCKYKF 112 (116)
T ss_pred chhhhhhhhcccccCCceEEEEcCccceee
Confidence 76 4456888889877 88887643
No 34
>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=66.32 E-value=6.5 Score=27.86 Aligned_cols=37 Identities=22% Similarity=0.490 Sum_probs=26.1
Q ss_pred CCCcccccCCcccccccccCCCCCcccchhHHHHHhhC
Q psy8832 93 RSGVSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHN 130 (144)
Q Consensus 93 ~~~~~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~ 130 (144)
..+..|.+|+.. -|.|-.-+-|-.||-.|.-..+..|
T Consensus 11 ~~N~~CaDCg~~-~p~w~s~~~GiflC~~Cag~HR~lg 47 (116)
T PF01412_consen 11 PGNKVCADCGAP-NPTWASLNYGIFLCLECAGIHRSLG 47 (116)
T ss_dssp TTCTB-TTT-SB-S--EEETTTTEEE-HHHHHHHHHHT
T ss_pred cCcCcCCCCCCC-CCCEEEeecChhhhHHHHHHHHHhc
Confidence 355799999854 4589988889999999998888777
No 35
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=66.30 E-value=2.8 Score=32.84 Aligned_cols=31 Identities=29% Similarity=0.522 Sum_probs=23.7
Q ss_pred cccccCCCCCCCeeeeCCCCCcccccccccc
Q psy8832 38 KECVNCAANSTPLWRRDGTGHHLCNACGLYN 68 (144)
Q Consensus 38 ~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~ 68 (144)
-.|..|+...|-+-..+..-..-|+|||-..
T Consensus 99 V~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVLMLRCDACGAHR 129 (201)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCCc
Confidence 5799999999998765332246899999854
No 36
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=66.09 E-value=2.2 Score=30.53 Aligned_cols=29 Identities=34% Similarity=0.595 Sum_probs=21.8
Q ss_pred cccccCCcccccccccCCCCCcccchhHH
Q psy8832 96 VSCANCSTTCTTLWRRNNNGEPVCNACGL 124 (144)
Q Consensus 96 ~~C~nC~t~~t~~WR~~~~g~~lCnaCgl 124 (144)
-.|..|+..+|-+=+.+..-...|+|||.
T Consensus 81 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 37999999999997753222445999984
No 37
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=65.97 E-value=3.5 Score=30.07 Aligned_cols=29 Identities=28% Similarity=0.540 Sum_probs=23.2
Q ss_pred cccccCCCCCCCeeeeCCCCCcccccccc
Q psy8832 38 KECVNCAANSTPLWRRDGTGHHLCNACGL 66 (144)
Q Consensus 38 ~~C~~C~t~~tp~wrr~~~g~~lCnaCgl 66 (144)
-.|..|+..+|-+-..+..-..-|+|||-
T Consensus 94 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred EEcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 46999999999887774444569999996
No 38
>PLN02400 cellulose synthase
Probab=64.75 E-value=6.8 Score=38.05 Aligned_cols=28 Identities=25% Similarity=0.611 Sum_probs=18.0
Q ss_pred CCCcccccCCCCCCCeeeeCCCCCc--ccccccc
Q psy8832 35 MDIKECVNCAANSTPLWRRDGTGHH--LCNACGL 66 (144)
Q Consensus 35 ~~~~~C~~C~t~~tp~wrr~~~g~~--lCnaCgl 66 (144)
....+|-.||-.... +.+|++ .||+|+.
T Consensus 34 ~~gqiCqICGD~VG~----t~dGe~FVAC~eCaF 63 (1085)
T PLN02400 34 LNGQICQICGDDVGV----TETGDVFVACNECAF 63 (1085)
T ss_pred cCCceeeecccccCc----CCCCCEEEEEccCCC
Confidence 344589999976554 356653 6666655
No 39
>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=64.47 E-value=3.5 Score=29.11 Aligned_cols=37 Identities=35% Similarity=0.747 Sum_probs=30.7
Q ss_pred CcccccCCCCCCCeeeeCCCCCcccccccccccccCCC
Q psy8832 37 IKECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVN 74 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~g~~ 74 (144)
...|..||. .-|.|-.-.-|-++|..|.-.++.-|.+
T Consensus 3 N~~CaDC~~-~~p~w~s~~~GifvC~~CsgiHR~lg~h 39 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLGVFLCIECSGIHRSLGVH 39 (112)
T ss_pred CCcccCCCC-CCCCcEEeccceeEhHHhHHHHHhcCCC
Confidence 468999998 5699998888999999998887776644
No 40
>KOG1598|consensus
Probab=63.74 E-value=4.3 Score=36.39 Aligned_cols=29 Identities=34% Similarity=0.747 Sum_probs=22.3
Q ss_pred cccccCCCCCCCeeeeCCCCCcccccccccc
Q psy8832 38 KECVNCAANSTPLWRRDGTGHHLCNACGLYN 68 (144)
Q Consensus 38 ~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~ 68 (144)
+.|.|||.+..- ++-.+|...|.+||.-.
T Consensus 1 ~~C~~C~~s~fe--~d~a~g~~~C~~CG~v~ 29 (521)
T KOG1598|consen 1 MVCKNCGGSNFE--RDEATGNLYCTACGTVL 29 (521)
T ss_pred CcCCCCCCCCcc--cccccCCceecccccee
Confidence 479999987655 33457889999999854
No 41
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=63.73 E-value=2.5 Score=31.18 Aligned_cols=29 Identities=28% Similarity=0.606 Sum_probs=21.5
Q ss_pred cccccCCcccccccccCCCCCcccchhHH
Q psy8832 96 VSCANCSTTCTTLWRRNNNGEPVCNACGL 124 (144)
Q Consensus 96 ~~C~nC~t~~t~~WR~~~~g~~lCnaCgl 124 (144)
-.|..|+..+|-+-+.+.--...|+|||-
T Consensus 98 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa 126 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVSLLKCEACGA 126 (133)
T ss_pred EECCCCCCCCcEEEEeCCeEEEecccCCC
Confidence 37999999999987643221345999986
No 42
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=63.60 E-value=5.4 Score=23.08 Aligned_cols=28 Identities=32% Similarity=0.889 Sum_probs=19.9
Q ss_pred ccccCCCCCCCeee-eCCCCCcccccccc
Q psy8832 39 ECVNCAANSTPLWR-RDGTGHHLCNACGL 66 (144)
Q Consensus 39 ~C~~C~t~~tp~wr-r~~~g~~lCnaCgl 66 (144)
-|.+||.+..=.|. ++..|..+|+.|+.
T Consensus 5 pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 5 PCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred CCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 48889886655554 24567889999974
No 43
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=62.61 E-value=5.6 Score=33.52 Aligned_cols=39 Identities=33% Similarity=0.697 Sum_probs=31.9
Q ss_pred CCCCcccccCCCCCCCeeeeCCCCCcccccccccccccCC
Q psy8832 34 NMDIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGV 73 (144)
Q Consensus 34 ~~~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~g~ 73 (144)
......|..||+.. |.|-.=.-|-+||-.|---+|.-|.
T Consensus 17 ~~~Nk~CaDCga~~-P~W~S~nlGvfiCi~CagvHRsLGv 55 (319)
T COG5347 17 DSSNKKCADCGAPN-PTWASVNLGVFLCIDCAGVHRSLGV 55 (319)
T ss_pred ccccCccccCCCCC-CceEecccCeEEEeecchhhhcccc
Confidence 34567899999999 9999888999999999765555553
No 44
>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=62.50 E-value=4.1 Score=28.90 Aligned_cols=38 Identities=34% Similarity=0.652 Sum_probs=26.1
Q ss_pred CCCcccccCCCCCCCeeeeCCCCCcccccccccccccCC
Q psy8832 35 MDIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGV 73 (144)
Q Consensus 35 ~~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~g~ 73 (144)
.....|..||+ .-|.|-.-.-|-++|..|.-.++.-|.
T Consensus 11 ~~N~~CaDCg~-~~p~w~s~~~GiflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 11 PGNKVCADCGA-PNPTWASLNYGIFLCLECAGIHRSLGV 48 (116)
T ss_dssp TTCTB-TTT-S-BS--EEETTTTEEE-HHHHHHHHHHTT
T ss_pred cCcCcCCCCCC-CCCCEEEeecChhhhHHHHHHHHHhcc
Confidence 44578999994 456999888899999999887776664
No 45
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=62.34 E-value=6.1 Score=32.77 Aligned_cols=30 Identities=27% Similarity=0.606 Sum_probs=21.7
Q ss_pred CCcccccCCCCCCCeeeeCCCCCccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLY 67 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly 67 (144)
....|.+||. ++.--....|+++|..||+-
T Consensus 10 ~~~~Cp~Cg~--~~iv~d~~~Ge~vC~~CG~V 39 (310)
T PRK00423 10 EKLVCPECGS--DKLIYDYERGEIVCADCGLV 39 (310)
T ss_pred cCCcCcCCCC--CCeeEECCCCeEeecccCCc
Confidence 4457999995 34444456788999999984
No 46
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=62.14 E-value=3.4 Score=23.48 Aligned_cols=28 Identities=25% Similarity=0.628 Sum_probs=12.1
Q ss_pred ccccCCcccccccccCCCC-CcccchhHH
Q psy8832 97 SCANCSTTCTTLWRRNNNG-EPVCNACGL 124 (144)
Q Consensus 97 ~C~nC~t~~t~~WR~~~~g-~~lCnaCgl 124 (144)
-|.+|+..-+..=-.+++- +.+|.+||.
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCC
Confidence 4778877532221112222 677998874
No 47
>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=60.75 E-value=2.3 Score=24.95 Aligned_cols=29 Identities=21% Similarity=0.526 Sum_probs=17.7
Q ss_pred cccccCCCCCCCe--eeeCCCCCcccccccc
Q psy8832 38 KECVNCAANSTPL--WRRDGTGHHLCNACGL 66 (144)
Q Consensus 38 ~~C~~C~t~~tp~--wrr~~~g~~lCnaCgl 66 (144)
+.|+-||.+.+.. .-.|++|...|+.|..
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 5799999887643 3367767789999965
No 48
>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=58.90 E-value=9.6 Score=22.57 Aligned_cols=26 Identities=23% Similarity=0.535 Sum_probs=17.8
Q ss_pred cccccCCCCCCCeeeeCCCCCccccccc
Q psy8832 38 KECVNCAANSTPLWRRDGTGHHLCNACG 65 (144)
Q Consensus 38 ~~C~~C~t~~tp~wrr~~~g~~lCnaCg 65 (144)
.+|..||.+ ...+. ...+.+.|++|+
T Consensus 19 ~~CP~Cg~~-~~~~~-~~~~~~~C~~C~ 44 (46)
T PF12760_consen 19 FVCPHCGST-KHYRL-KTRGRYRCKACR 44 (46)
T ss_pred CCCCCCCCe-eeEEe-CCCCeEECCCCC
Confidence 579999987 33333 335667888886
No 49
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=58.09 E-value=4.8 Score=29.34 Aligned_cols=28 Identities=29% Similarity=0.542 Sum_probs=22.3
Q ss_pred ccccCCcccccccccCCCCCcccchhHH
Q psy8832 97 SCANCSTTCTTLWRRNNNGEPVCNACGL 124 (144)
Q Consensus 97 ~C~nC~t~~t~~WR~~~~g~~lCnaCgl 124 (144)
.|..|+..+|-+-..+..-...|+|||-
T Consensus 95 lC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 95 LCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp SCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred EcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 7999999999997764333555999984
No 50
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=56.90 E-value=5.2 Score=23.92 Aligned_cols=40 Identities=18% Similarity=0.247 Sum_probs=24.7
Q ss_pred ccccCCcccccccccCCCCCcccchhHHHHHhhCCCCccccccccc
Q psy8832 97 SCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHNVFTILFYNITKA 142 (144)
Q Consensus 97 ~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~~~Rp~~l~~~~~ 142 (144)
.|.+|+.+.+.. ..+..-|..||-.-- =+.||..++.-+|
T Consensus 4 ~C~~Cg~~~~~~----~~~~irC~~CG~rIl--yK~R~~~~~~~~A 43 (44)
T smart00659 4 ICGECGRENEIK----SKDVVRCRECGYRIL--YKKRTKRLVEVKA 43 (44)
T ss_pred ECCCCCCEeecC----CCCceECCCCCceEE--EEeCCCceEEEEc
Confidence 699999977654 234567999985221 2455555555444
No 51
>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=56.73 E-value=8.6 Score=24.34 Aligned_cols=29 Identities=21% Similarity=0.558 Sum_probs=20.3
Q ss_pred CCcccccCCCCCCCeeeeCCCCCccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLY 67 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly 67 (144)
.+..|+.||..... +.......|..||..
T Consensus 27 TSq~C~~CG~~~~~---~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK---RRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCccccccc---ccccceEEcCCCCCE
Confidence 56789999976655 122235799999985
No 52
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=54.73 E-value=2.2 Score=34.90 Aligned_cols=71 Identities=27% Similarity=0.505 Sum_probs=33.5
Q ss_pred CcccccCCCCCCCeeeeCCC--C--CcccccccccccccCCCCCCccccchhhhhhcCCCCCCcccccCCccccc-ccc-
Q psy8832 37 IKECVNCAANSTPLWRRDGT--G--HHLCNACGLYNRINGVNRPPVRTNQKKALQQTGNKRSGVSCANCSTTCTT-LWR- 110 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr~~~--g--~~lCnaCgly~r~~g~~RP~~k~kkkka~~~s~~k~~~~~C~nC~t~~t~-~WR- 110 (144)
...|-.||+.-.--+-++.. | ...|.-|+--|.... ..|.+|+.++.- +|-
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R-----------------------~~Cp~Cg~~~~~~l~~~ 228 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVR-----------------------IKCPYCGNTDHEKLEYF 228 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE--T-----------------------TS-TTT---SS-EEE--
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecC-----------------------CCCcCCCCCCCcceeeE
Confidence 35899999877666666665 7 358999998665321 169999776644 442
Q ss_pred --cCCCC--CcccchhHHHHHhhC
Q psy8832 111 --RNNNG--EPVCNACGLYFKLHN 130 (144)
Q Consensus 111 --~~~~g--~~lCnaCglyy~~~~ 130 (144)
.+..+ -.+|..|+-|.|.--
T Consensus 229 ~~e~~~~~rve~C~~C~~YlK~vd 252 (290)
T PF04216_consen 229 TVEGEPAYRVEVCESCGSYLKTVD 252 (290)
T ss_dssp ------SEEEEEETTTTEEEEEEE
T ss_pred ecCCCCcEEEEECCcccchHHHHh
Confidence 12233 446999998877543
No 53
>PHA00626 hypothetical protein
Probab=53.97 E-value=9.9 Score=24.22 Aligned_cols=32 Identities=19% Similarity=0.479 Sum_probs=21.8
Q ss_pred ccccCCCCCCCe--eeeCCCCCcccccccccccc
Q psy8832 39 ECVNCAANSTPL--WRRDGTGHHLCNACGLYNRI 70 (144)
Q Consensus 39 ~C~~C~t~~tp~--wrr~~~g~~lCnaCgly~r~ 70 (144)
.|.+||..+-.. --+++...+.|..||.++.+
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeech
Confidence 689999754331 11355677899999997654
No 54
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=53.00 E-value=6.6 Score=25.04 Aligned_cols=26 Identities=19% Similarity=0.300 Sum_probs=19.4
Q ss_pred CCcccccCCCCCCCeeeeCCCCCcccccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRI 70 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~ 70 (144)
...+|.+||+..-| +.+|. ||.|...
T Consensus 26 ~~~~c~~cg~~~~p--------H~vc~-cG~Y~gr 51 (60)
T PRK01110 26 TLSVDKTTGEYHLP--------HHVSP-KGYYKGR 51 (60)
T ss_pred ceeEcCCCCceecc--------ceecC-CcccCCe
Confidence 35689999977766 46899 9988543
No 55
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=52.90 E-value=7.4 Score=22.73 Aligned_cols=7 Identities=29% Similarity=1.260 Sum_probs=3.2
Q ss_pred ccccCCc
Q psy8832 97 SCANCST 103 (144)
Q Consensus 97 ~C~nC~t 103 (144)
.|.+|+.
T Consensus 28 ~CP~Cg~ 34 (42)
T PF09723_consen 28 PCPECGS 34 (42)
T ss_pred cCCCCCC
Confidence 4444444
No 56
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=52.72 E-value=11 Score=26.89 Aligned_cols=89 Identities=22% Similarity=0.587 Sum_probs=47.2
Q ss_pred CcccccCCCCCCCeeeeC-CCCCcccccccccccccCC--CCC--C-ccccchhhh-----hhcCCCC---CCcccccCC
Q psy8832 37 IKECVNCAANSTPLWRRD-GTGHHLCNACGLYNRINGV--NRP--P-VRTNQKKAL-----QQTGNKR---SGVSCANCS 102 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr~-~~g~~lCnaCgly~r~~g~--~RP--~-~k~kkkka~-----~~s~~k~---~~~~C~nC~ 102 (144)
..-|..||.---| +++ ..+...|-.||.-+..... .+- . ..+.++... ....... ....|..|+
T Consensus 2 m~FCp~Cgsll~p--~~~~~~~~l~C~kCgye~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg 79 (113)
T COG1594 2 MRFCPKCGSLLYP--KKDDEGGKLVCRKCGYEEEASNKKVYRYSVKEAVEKKKEVVLVVEDETQGAKTLPTAKEKCPKCG 79 (113)
T ss_pred ccccCCccCeeEE--eEcCCCcEEECCCCCcchhccccceeEEEEeeccCCcceeeeeecccccCccccccccccCCCCC
Confidence 3568888865555 233 3346789999886554421 000 0 000000000 0111111 124699999
Q ss_pred ccccccc----ccCCCCC---cccchhHHHHH
Q psy8832 103 TTCTTLW----RRNNNGE---PVCNACGLYFK 127 (144)
Q Consensus 103 t~~t~~W----R~~~~g~---~lCnaCglyy~ 127 (144)
..+--.| |.+.++. ..|-.||-.|+
T Consensus 80 ~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 80 NKEAYYWQLQTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred CceeEEEeeehhccCCCceEEEEecccCCEee
Confidence 9998877 5555553 34999997665
No 57
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=52.59 E-value=9.9 Score=25.08 Aligned_cols=37 Identities=24% Similarity=0.376 Sum_probs=27.4
Q ss_pred CcccccCCCCCCCeeeeCCC-CCcccccccccccccCC
Q psy8832 37 IKECVNCAANSTPLWRRDGT-GHHLCNACGLYNRINGV 73 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr~~~-g~~lCnaCgly~r~~g~ 73 (144)
+-+|..|++..|-.|.+..+ ...-|-+||........
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred CccCCCCcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence 45799999998887665544 45699999997665433
No 58
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=52.17 E-value=8.9 Score=27.26 Aligned_cols=50 Identities=20% Similarity=0.509 Sum_probs=30.4
Q ss_pred CCcccccCCCCCCCeeeeCCCCCcccccccccccccCCCCCCccccchhhhhhcCCCCCCcccccCCcccccccccCCCC
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVNRPPVRTNQKKALQQTGNKRSGVSCANCSTTCTTLWRRNNNG 115 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~g~~RP~~k~kkkka~~~s~~k~~~~~C~nC~t~~t~~WR~~~~g 115 (144)
....|..|+..-+.+ ++.| .+|..|..+ +|..|+.. .....
T Consensus 53 ~~~~C~~C~~~fg~l---~~~~-~~C~~C~~~-----------------------------VC~~C~~~------~~~~~ 93 (118)
T PF02318_consen 53 GERHCARCGKPFGFL---FNRG-RVCVDCKHR-----------------------------VCKKCGVY------SKKEP 93 (118)
T ss_dssp CCSB-TTTS-BCSCT---STTC-EEETTTTEE-----------------------------EETTSEEE------TSSSC
T ss_pred CCcchhhhCCccccc---CCCC-CcCCcCCcc-----------------------------ccCccCCc------CCCCC
Confidence 456899998765544 3333 477777652 78888874 22334
Q ss_pred CcccchhHH
Q psy8832 116 EPVCNACGL 124 (144)
Q Consensus 116 ~~lCnaCgl 124 (144)
..+|+.|.-
T Consensus 94 ~WlC~vC~k 102 (118)
T PF02318_consen 94 IWLCKVCQK 102 (118)
T ss_dssp CEEEHHHHH
T ss_pred CEEChhhHH
Confidence 578888864
No 59
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=51.74 E-value=5.1 Score=31.37 Aligned_cols=29 Identities=31% Similarity=0.598 Sum_probs=21.6
Q ss_pred cccccCCcccccccccCCCCCcccchhHH
Q psy8832 96 VSCANCSTTCTTLWRRNNNGEPVCNACGL 124 (144)
Q Consensus 96 ~~C~nC~t~~t~~WR~~~~g~~lCnaCgl 124 (144)
-.|..|+..+|-|=+.+..-...|+|||-
T Consensus 99 V~C~~C~~pdT~l~k~~~~~~l~C~aCGa 127 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVLMLRCDACGA 127 (201)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCC
Confidence 47999999999996643221445999986
No 60
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=48.62 E-value=7.1 Score=25.25 Aligned_cols=34 Identities=32% Similarity=0.746 Sum_probs=26.0
Q ss_pred CCcccccCCccccc-ccccCCCCCcccchhHHHHH
Q psy8832 94 SGVSCANCSTTCTT-LWRRNNNGEPVCNACGLYFK 127 (144)
Q Consensus 94 ~~~~C~nC~t~~t~-~WR~~~~g~~lCnaCglyy~ 127 (144)
-+..|.-|.+..|. +||.+.-.-.-|-+||...+
T Consensus 9 AGA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~ 43 (66)
T COG3529 9 AGAVCPACQAQDTLAMWRENNVEIVECVKCGHHMR 43 (66)
T ss_pred ccCCCcccchhhHHHHHHhcCCceEehhhcchHhh
Confidence 45689999988887 78876655556999998554
No 61
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=48.54 E-value=9.3 Score=19.62 Aligned_cols=7 Identities=43% Similarity=1.474 Sum_probs=3.8
Q ss_pred ccccccc
Q psy8832 59 HLCNACG 65 (144)
Q Consensus 59 ~lCnaCg 65 (144)
.+|..||
T Consensus 14 ~fC~~CG 20 (23)
T PF13240_consen 14 KFCPNCG 20 (23)
T ss_pred cchhhhC
Confidence 3555555
No 62
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=48.04 E-value=12 Score=31.00 Aligned_cols=29 Identities=24% Similarity=0.625 Sum_probs=20.2
Q ss_pred cccccCCCCCCCeeeeCCCCCcccccccccc
Q psy8832 38 KECVNCAANSTPLWRRDGTGHHLCNACGLYN 68 (144)
Q Consensus 38 ~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~ 68 (144)
..|.+||.+ -.-..-..|+.+|-.||+--
T Consensus 2 ~~CpeCg~~--~~~~d~~~ge~VC~~CG~Vi 30 (285)
T COG1405 2 MSCPECGST--NIITDYERGEIVCADCGLVL 30 (285)
T ss_pred CCCCCCCCc--cceeeccCCeEEeccCCEEe
Confidence 469999987 22222346889999999853
No 63
>KOG3740|consensus
Probab=47.82 E-value=7.2 Score=35.83 Aligned_cols=30 Identities=30% Similarity=0.762 Sum_probs=26.1
Q ss_pred CcccccCCcccccccccCCCC----CcccchhHH
Q psy8832 95 GVSCANCSTTCTTLWRRNNNG----EPVCNACGL 124 (144)
Q Consensus 95 ~~~C~nC~t~~t~~WR~~~~g----~~lCnaCgl 124 (144)
+-.|..|.+..||.|+.-..+ ..+|+.|.-
T Consensus 462 P~~caqcktdftp~wk~ekstq~d~~i~cE~cvt 495 (706)
T KOG3740|consen 462 PYACAQCKTDFTPAWKKEKSTQADAAIVCENCVT 495 (706)
T ss_pred chhhhhcccccccccccccccCcchHHHHHhhhh
Confidence 568999999999999987666 889999965
No 64
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=46.87 E-value=13 Score=23.86 Aligned_cols=33 Identities=21% Similarity=0.410 Sum_probs=24.5
Q ss_pred CcccccCCCCCCCeeee-CCCCCccccccccccc
Q psy8832 37 IKECVNCAANSTPLWRR-DGTGHHLCNACGLYNR 69 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr-~~~g~~lCnaCgly~r 69 (144)
+-+|..|++-.|-.|.+ ++....-|-+||...+
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~ 42 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNIELVECVECGYQEQ 42 (59)
T ss_pred cccCCCCcCccEEEEEEeCCceEEEeccCCCccc
Confidence 45799999988876554 4444579999998654
No 65
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=45.63 E-value=11 Score=23.87 Aligned_cols=17 Identities=12% Similarity=0.487 Sum_probs=7.1
Q ss_pred CCCCcccccCCCCCCCe
Q psy8832 34 NMDIKECVNCAANSTPL 50 (144)
Q Consensus 34 ~~~~~~C~~C~t~~tp~ 50 (144)
+.....|..|+..-+-+
T Consensus 6 d~~~~~C~~C~~~F~~~ 22 (69)
T PF01363_consen 6 DSEASNCMICGKKFSLF 22 (69)
T ss_dssp GGG-SB-TTT--B-BSS
T ss_pred CCCCCcCcCcCCcCCCc
Confidence 34556788888766443
No 66
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=45.31 E-value=12 Score=23.70 Aligned_cols=26 Identities=35% Similarity=0.944 Sum_probs=19.5
Q ss_pred CCcccccCCCCCCCeeeeCCCCCccccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLYNR 69 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r 69 (144)
...+|.+||...-| +-+|..||.|..
T Consensus 26 ~~~~c~~cG~~~l~--------Hrvc~~cg~Y~g 51 (57)
T COG0333 26 TLSVCPNCGEYKLP--------HRVCLKCGYYKG 51 (57)
T ss_pred cceeccCCCCcccC--------ceEcCCCCCccC
Confidence 35689999976655 468999998754
No 67
>KOG3740|consensus
Probab=44.79 E-value=7.6 Score=35.69 Aligned_cols=36 Identities=22% Similarity=0.652 Sum_probs=29.9
Q ss_pred CCCcccccCCCCCCCeeeeCCCC----Ccccccccccccc
Q psy8832 35 MDIKECVNCAANSTPLWRRDGTG----HHLCNACGLYNRI 70 (144)
Q Consensus 35 ~~~~~C~~C~t~~tp~wrr~~~g----~~lCnaCgly~r~ 70 (144)
.+..+|..|.|..||.|+.-+.+ .++|.+|.-...+
T Consensus 460 ~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSnqk 499 (706)
T KOG3740|consen 460 TEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSNQK 499 (706)
T ss_pred CCchhhhhcccccccccccccccCcchHHHHHhhhhhccc
Confidence 35678999999999999988777 6899999875443
No 68
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=44.47 E-value=15 Score=31.72 Aligned_cols=44 Identities=16% Similarity=0.341 Sum_probs=34.0
Q ss_pred CCCcccccCCcccccccccCCCCCcccchhHHHHHhhCCC----Ccccc
Q psy8832 93 RSGVSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHNVF----TILFY 137 (144)
Q Consensus 93 ~~~~~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~~~----Rp~~l 137 (144)
.-+..|..|+... |.|---+-|-.||-.|.=.-|..|++ |.++|
T Consensus 20 PgNk~CaDCga~n-PtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltL 67 (395)
T PLN03114 20 SDNKICFDCNAKN-PTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNL 67 (395)
T ss_pred cCCCcCccCCCCC-CCceeeccceeehhhhhHhhccCCCCCceeecccC
Confidence 3566899999764 99998888999999998766666643 55555
No 69
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=44.46 E-value=13 Score=31.40 Aligned_cols=37 Identities=24% Similarity=0.497 Sum_probs=30.4
Q ss_pred CCCcccccCCcccccccccCCCCCcccchhHHHHHhhC
Q psy8832 93 RSGVSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHN 130 (144)
Q Consensus 93 ~~~~~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~ 130 (144)
..+..|..|+... |.|-.-+-|-.||-.|.---|.-|
T Consensus 18 ~~Nk~CaDCga~~-P~W~S~nlGvfiCi~CagvHRsLG 54 (319)
T COG5347 18 SSNKKCADCGAPN-PTWASVNLGVFLCIDCAGVHRSLG 54 (319)
T ss_pred cccCccccCCCCC-CceEecccCeEEEeecchhhhccc
Confidence 4567999999999 999988899999999976444444
No 70
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=44.11 E-value=17 Score=21.57 Aligned_cols=30 Identities=23% Similarity=0.560 Sum_probs=18.5
Q ss_pred ccccCCCCCCCeeeeCCC-CCcccccccccccc
Q psy8832 39 ECVNCAANSTPLWRRDGT-GHHLCNACGLYNRI 70 (144)
Q Consensus 39 ~C~~C~t~~tp~wrr~~~-g~~lCnaCgly~r~ 70 (144)
-|..||..-.+. .+.. ....|..||..+..
T Consensus 2 FCp~Cg~~l~~~--~~~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 2 FCPKCGNMLIPK--EGKEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCccccc--cCCCCCEEECCcCCCeEEC
Confidence 588999744332 1212 26799999975544
No 71
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=42.75 E-value=19 Score=25.56 Aligned_cols=32 Identities=25% Similarity=0.473 Sum_probs=20.6
Q ss_pred CCcccccCCCCCCCeeeeCCCCCccccccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRIN 71 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~ 71 (144)
..++|.+||+.-.-|=| .| .+|.-||--+...
T Consensus 8 tKR~Cp~CG~kFYDLnk-~P---ivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNK-DP---IVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCCC-CC---ccCCCCCCccCcc
Confidence 46778888877666622 22 4688888755443
No 72
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=41.77 E-value=19 Score=18.85 Aligned_cols=23 Identities=26% Similarity=0.739 Sum_probs=11.2
Q ss_pred cccCCCCCCCeeeeCCCCCccccccc
Q psy8832 40 CVNCAANSTPLWRRDGTGHHLCNACG 65 (144)
Q Consensus 40 C~~C~t~~tp~wrr~~~g~~lCnaCg 65 (144)
|..||..-.|. ...-.+.|..||
T Consensus 1 C~sC~~~i~~r---~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPR---EQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCc---ccCceEeCCCCC
Confidence 45555544442 212245666666
No 73
>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=41.49 E-value=16 Score=21.78 Aligned_cols=27 Identities=19% Similarity=0.514 Sum_probs=15.6
Q ss_pred ccccCCCCCCCeeeeCC-CCCcccccccc
Q psy8832 39 ECVNCAANSTPLWRRDG-TGHHLCNACGL 66 (144)
Q Consensus 39 ~C~~C~t~~tp~wrr~~-~g~~lCnaCgl 66 (144)
.|.+||..-. .|+... +....|..||-
T Consensus 7 ~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFE-VLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeE-EEEecCCCCCCCCCCCCC
Confidence 5777775433 455432 23456777776
No 74
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=41.39 E-value=14 Score=30.99 Aligned_cols=47 Identities=26% Similarity=0.563 Sum_probs=29.6
Q ss_pred CCCCCCccccccCCCCccCCCCCcccccCCCCCCCeeeeCCCCC-cccccccc
Q psy8832 15 DGPFQAYLTVIDWPQNMMLNMDIKECVNCAANSTPLWRRDGTGH-HLCNACGL 66 (144)
Q Consensus 15 ~~~~~s~~~~~~~~~~~~~~~~~~~C~~C~t~~tp~wrr~~~g~-~lCnaCgl 66 (144)
..+.++.....+|+..+- .....|.|||-..|+- -++|. -+|.+||-
T Consensus 295 q~qaqaa~pa~t~~~~r~--~k~nfc~ncG~~~t~~---~~ng~a~fcp~cgq 342 (345)
T COG4260 295 QAQAQAAAPAATWPCARC--AKLNFCLNCGCGTTAD---FDNGKAKFCPECGQ 342 (345)
T ss_pred hhhhhhcCCcccCcchhc--cccccccccCcccccC---CccchhhhChhhcC
Confidence 345566667777776432 2334899999666662 13453 49999984
No 75
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=41.06 E-value=45 Score=24.26 Aligned_cols=37 Identities=22% Similarity=0.385 Sum_probs=24.3
Q ss_pred ccccCCCCCCCeeeeCCCCCccccccccc--ccccCCCCC
Q psy8832 39 ECVNCAANSTPLWRRDGTGHHLCNACGLY--NRINGVNRP 76 (144)
Q Consensus 39 ~C~~C~t~~tp~wrr~~~g~~lCnaCgly--~r~~g~~RP 76 (144)
.|.-||..+ ..+..+.+-.+.|..|+-| +..+|.++.
T Consensus 2 ~C~fC~~~s-~~~~~~~~~~w~C~~C~q~N~f~e~Gd~~d 40 (131)
T PF09779_consen 2 NCWFCGQNS-KVPYDNRNSNWTCPHCEQYNGFDEDGDITD 40 (131)
T ss_pred eeccCCCCC-CCCCCCCCCeeECCCCCCccCccccCCCCC
Confidence 588999765 4444454555899999886 344555544
No 76
>PLN02436 cellulose synthase A
Probab=40.82 E-value=27 Score=34.09 Aligned_cols=28 Identities=21% Similarity=0.554 Sum_probs=18.4
Q ss_pred CCCcccccCCCCCCCeeeeCCCCCc--ccccccc
Q psy8832 35 MDIKECVNCAANSTPLWRRDGTGHH--LCNACGL 66 (144)
Q Consensus 35 ~~~~~C~~C~t~~tp~wrr~~~g~~--lCnaCgl 66 (144)
....+|..||-.... +.+|++ -||.|+.
T Consensus 34 ~~~~iCqICGD~Vg~----t~dGe~FVACn~C~f 63 (1094)
T PLN02436 34 LSGQTCQICGDEIEL----TVDGEPFVACNECAF 63 (1094)
T ss_pred cCCccccccccccCc----CCCCCEEEeeccCCC
Confidence 345589999976544 355653 6777765
No 77
>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=39.97 E-value=11 Score=21.42 Aligned_cols=28 Identities=14% Similarity=0.450 Sum_probs=14.5
Q ss_pred CcccccCCCCCCCeeeeCCCCCcccccc
Q psy8832 37 IKECVNCAANSTPLWRRDGTGHHLCNAC 64 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr~~~g~~lCnaC 64 (144)
.+.|..|+......|-...=+..+|+.|
T Consensus 3 ~~~C~eC~~~f~dSyL~~~F~~~VCD~C 30 (34)
T PF01286_consen 3 YPKCDECGKPFMDSYLLNNFDLPVCDKC 30 (34)
T ss_dssp -EE-TTT--EES-SSCCCCTS-S--TTT
T ss_pred CchHhHhCCHHHHHHHHHhCCccccccc
Confidence 4578899987766666566666788888
No 78
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=39.85 E-value=9.8 Score=22.09 Aligned_cols=29 Identities=28% Similarity=0.678 Sum_probs=14.4
Q ss_pred ccccCCccccccc----ccCCCC---CcccchhHHH
Q psy8832 97 SCANCSTTCTTLW----RRNNNG---EPVCNACGLY 125 (144)
Q Consensus 97 ~C~nC~t~~t~~W----R~~~~g---~~lCnaCgly 125 (144)
.|.+|+-.+...| |.+.++ -.+|-.||-.
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence 3566665554444 334444 2336666643
No 79
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=38.87 E-value=19 Score=23.15 Aligned_cols=14 Identities=21% Similarity=0.733 Sum_probs=11.4
Q ss_pred ccccCCCCC-CCeee
Q psy8832 39 ECVNCAANS-TPLWR 52 (144)
Q Consensus 39 ~C~~C~t~~-tp~wr 52 (144)
.|.+||+++ |..|.
T Consensus 17 ~CP~Cgs~~~T~~W~ 31 (61)
T PRK08351 17 RCPVCGSRDLSDEWF 31 (61)
T ss_pred cCCCCcCCccccccc
Confidence 699999887 77776
No 80
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=38.70 E-value=17 Score=20.87 Aligned_cols=28 Identities=25% Similarity=0.663 Sum_probs=13.5
Q ss_pred ccccCCccccccc----ccCCCC---CcccchhHH
Q psy8832 97 SCANCSTTCTTLW----RRNNNG---EPVCNACGL 124 (144)
Q Consensus 97 ~C~nC~t~~t~~W----R~~~~g---~~lCnaCgl 124 (144)
.|.+|+..+.-.| |.+.++ -..|..||-
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~ 36 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGH 36 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCC
Confidence 4667776665554 334444 223777764
No 81
>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=38.09 E-value=22 Score=23.58 Aligned_cols=31 Identities=26% Similarity=0.593 Sum_probs=20.5
Q ss_pred cccccCCcccccccccCCCCCcccchhHHHHHhhC
Q psy8832 96 VSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHN 130 (144)
Q Consensus 96 ~~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~ 130 (144)
..|.-|+...+-. .-|-..|+||..+|+++-
T Consensus 3 ~~C~VCg~~a~g~----hyGv~sC~aC~~FFRR~v 33 (78)
T cd07172 3 KICLVCSDEASGC----HYGVLTCGSCKVFFKRAV 33 (78)
T ss_pred CCCeecCCcCcce----EECceeehhhHHhHHHHe
Confidence 3577787533222 224567999999999874
No 82
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=38.00 E-value=21 Score=21.84 Aligned_cols=27 Identities=22% Similarity=0.593 Sum_probs=18.5
Q ss_pred CCcccccCCCCCCCeeeeCCCCCcccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGL 66 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgl 66 (144)
..+.|.+||.+ +.... .+...|..||+
T Consensus 19 ~~~fCP~Cg~~---~m~~~-~~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSG---FMAEH-LDRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcc---hhecc-CCcEECCCcCC
Confidence 45689999964 33322 25678999987
No 83
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=37.39 E-value=16 Score=21.49 Aligned_cols=26 Identities=27% Similarity=0.763 Sum_probs=13.5
Q ss_pred ccccCCCCCCCe-eee-CCCCCcccccc
Q psy8832 39 ECVNCAANSTPL-WRR-DGTGHHLCNAC 64 (144)
Q Consensus 39 ~C~~C~t~~tp~-wrr-~~~g~~lCnaC 64 (144)
-|..||.+.-=. |.. ...|...|+.|
T Consensus 5 pCP~CGG~DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp --TTTT-TTTEEEETT----S-EEETTT
T ss_pred CCCCCcCccccccCcCcccCCCEECCCC
Confidence 488888755443 542 34578899999
No 84
>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=37.15 E-value=27 Score=19.47 Aligned_cols=24 Identities=25% Similarity=0.522 Sum_probs=13.0
Q ss_pred ccccCCCCCCCeeeeCCCCCcccccccc
Q psy8832 39 ECVNCAANSTPLWRRDGTGHHLCNACGL 66 (144)
Q Consensus 39 ~C~~C~t~~tp~wrr~~~g~~lCnaCgl 66 (144)
.|..||+...- .+....-|..||-
T Consensus 2 ~C~~Cg~~~~~----~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVEL----KPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-B----STSSTSSBSSSS-
T ss_pred CCCcCCCeeEc----CCCCcEECCcCCC
Confidence 47778776652 1222357777775
No 85
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=36.97 E-value=24 Score=30.51 Aligned_cols=39 Identities=36% Similarity=0.702 Sum_probs=31.2
Q ss_pred CCCcccccCCCCCCCeeeeCCCCCcccccccccccccCCC
Q psy8832 35 MDIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVN 74 (144)
Q Consensus 35 ~~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~g~~ 74 (144)
.....|..||.. -|.|-.-.-|-++|..|.=.++.-|.+
T Consensus 20 PgNk~CaDCga~-nPtWASvn~GIFLCl~CSGVHRsLGvH 58 (395)
T PLN03114 20 SDNKICFDCNAK-NPTWASVTYGIFLCIDCSAVHRSLGVH 58 (395)
T ss_pred cCCCcCccCCCC-CCCceeeccceeehhhhhHhhccCCCC
Confidence 356789999976 499998888999999998776665543
No 86
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=36.66 E-value=19 Score=20.13 Aligned_cols=28 Identities=25% Similarity=0.641 Sum_probs=12.0
Q ss_pred ccccCCcccccccccCCCCCcccchhHH
Q psy8832 97 SCANCSTTCTTLWRRNNNGEPVCNACGL 124 (144)
Q Consensus 97 ~C~nC~t~~t~~WR~~~~g~~lCnaCgl 124 (144)
.|.+|+...+.+-.-.......|-.||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 4555655443321111122344666654
No 87
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=36.52 E-value=28 Score=29.14 Aligned_cols=31 Identities=29% Similarity=0.558 Sum_probs=23.0
Q ss_pred cccccCCCCCCC-eeeeCCCCCcccccccccccc
Q psy8832 38 KECVNCAANSTP-LWRRDGTGHHLCNACGLYNRI 70 (144)
Q Consensus 38 ~~C~~C~t~~tp-~wrr~~~g~~lCnaCgly~r~ 70 (144)
+.|+.|...+|. --.-+.+| +||+|-.|..+
T Consensus 2 ~~C~~C~~~~t~p~i~fd~~G--vC~~C~~~~~~ 33 (343)
T TIGR03573 2 KFCKRCVMPTTRPGITFDEDG--VCSACRNFEEK 33 (343)
T ss_pred CcCCCCCCCCCCCCeeECCCC--CchhhhhHHhh
Confidence 579999976654 34456666 99999998754
No 88
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=36.33 E-value=28 Score=33.88 Aligned_cols=28 Identities=29% Similarity=0.719 Sum_probs=19.2
Q ss_pred CCCcccccCCCCCCCeeeeCCCCCc--ccccccc
Q psy8832 35 MDIKECVNCAANSTPLWRRDGTGHH--LCNACGL 66 (144)
Q Consensus 35 ~~~~~C~~C~t~~tp~wrr~~~g~~--lCnaCgl 66 (144)
....+|..||-.... +.+|++ -||+|+.
T Consensus 13 ~~~~~c~iCGd~vg~----~~~Ge~FVAC~eC~f 42 (1044)
T PLN02915 13 ADAKTCRVCGDEVGV----KEDGQPFVACHVCGF 42 (1044)
T ss_pred CCcchhhccccccCc----CCCCCEEEEeccCCC
Confidence 356789999976654 456653 6777765
No 89
>KOG0703|consensus
Probab=35.32 E-value=23 Score=29.47 Aligned_cols=34 Identities=32% Similarity=0.681 Sum_probs=28.1
Q ss_pred CCCcccccCCCCCCCeeeeCCCCCccccccccccc
Q psy8832 35 MDIKECVNCAANSTPLWRRDGTGHHLCNACGLYNR 69 (144)
Q Consensus 35 ~~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r 69 (144)
...+.|..||+. .|.|-.=.-|-++|--|-=-++
T Consensus 23 ~~N~~CADC~a~-~P~WaSwnlGvFiC~~C~giHR 56 (287)
T KOG0703|consen 23 PDNKVCADCGAK-GPRWASWNLGVFICLRCAGIHR 56 (287)
T ss_pred cccCcccccCCC-CCCeEEeecCeEEEeecccccc
Confidence 357899999998 9999988899999999854333
No 90
>KOG0706|consensus
Probab=35.26 E-value=23 Score=31.29 Aligned_cols=42 Identities=31% Similarity=0.611 Sum_probs=33.7
Q ss_pred CCCCCcccccCCCCCCCeeeeCCCCCcccccccccccccCCCC
Q psy8832 33 LNMDIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVNR 75 (144)
Q Consensus 33 ~~~~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~g~~R 75 (144)
..+..++|..||.. -|.|-.-..|-+||..|---+|.-|.+.
T Consensus 19 s~~~NKvCFDCgAk-nPtWaSVTYGIFLCiDCSAvHRnLGVHi 60 (454)
T KOG0706|consen 19 SQSENKVCFDCGAK-NPTWASVTYGIFLCIDCSAVHRNLGVHI 60 (454)
T ss_pred cCCCCceecccCCC-CCCceeecceEEEEEecchhhhccccce
Confidence 35577899999965 6889999999999999988766666543
No 91
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=35.18 E-value=33 Score=27.20 Aligned_cols=52 Identities=23% Similarity=0.496 Sum_probs=32.0
Q ss_pred cccCCCCCCCeeeeCCCCCcccccccccccccCCCCCCccccchhhhhhcCCCCCCcccccCCccccc-ccccC
Q psy8832 40 CVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVNRPPVRTNQKKALQQTGNKRSGVSCANCSTTCTT-LWRRN 112 (144)
Q Consensus 40 C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~g~~RP~~k~kkkka~~~s~~k~~~~~C~nC~t~~t~-~WR~~ 112 (144)
|..||....|+ .+| +|..|++- ..++...++ ...-..|..|+....+ .|...
T Consensus 1 C~~CG~~~~~~----~~~--lC~~C~~~------~~~i~ei~~---------~i~v~~C~~Cg~~~~~~~W~~~ 53 (236)
T PF04981_consen 1 CPRCGREIEPL----IDG--LCPDCYLK------RFDIIEIPD---------RIEVTICPKCGRYRIGGRWVDP 53 (236)
T ss_pred CCCCCCCCCCc----ccc--cChHHhcc------cCCeeecCC---------ccCceECCCCCCEECCCEeeec
Confidence 77899755553 233 99999882 223222110 1133489999988776 78766
No 92
>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=34.64 E-value=30 Score=23.56 Aligned_cols=33 Identities=30% Similarity=0.549 Sum_probs=22.1
Q ss_pred CCcccccCCcccccccccCCCCCcccchhHHHHHhhC
Q psy8832 94 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHN 130 (144)
Q Consensus 94 ~~~~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~ 130 (144)
+...|.-|+...+-. + -|-..|+||..+|+++-
T Consensus 5 ~~~~C~VCg~~~~g~-h---yGv~sC~aCk~FFRR~v 37 (90)
T cd07168 5 SPKLCSICEDKATGL-H---YGIITCEGCKGFFKRTV 37 (90)
T ss_pred cCCCCcccCCcCcce-E---ECceehhhhhHhhhhhh
Confidence 445688888643322 1 24567999999998864
No 93
>KOG0957|consensus
Probab=34.45 E-value=36 Score=30.84 Aligned_cols=59 Identities=22% Similarity=0.424 Sum_probs=39.5
Q ss_pred CCCCcccccCCCCCCCeeeeCCCCCcccccccccccccCCCCCCccccchhhhhhcCCCCCCcccccCCccc
Q psy8832 34 NMDIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVNRPPVRTNQKKALQQTGNKRSGVSCANCSTTC 105 (144)
Q Consensus 34 ~~~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~g~~RP~~k~kkkka~~~s~~k~~~~~C~nC~t~~ 105 (144)
....-.|..|..+.-. --.++|+.|-|.|.+.-.+.|+++.+++ ++..+-+|+.|...+
T Consensus 541 ~a~~ysCgiCkks~dQ------Hll~~CDtC~lhYHlGCL~PPLTR~Pkk-------~kn~gWqCsECdk~e 599 (707)
T KOG0957|consen 541 KAMNYSCGICKKSTDQ------HLLTQCDTCHLHYHLGCLSPPLTRLPKK-------NKNFGWQCSECDKNE 599 (707)
T ss_pred cccceeeeeeccchhh------HHHhhcchhhceeeccccCCccccCccc-------ccCcceeeccccccc
Confidence 3345567777643221 1236999999999988888888766543 345678999995544
No 94
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=34.43 E-value=18 Score=30.02 Aligned_cols=11 Identities=64% Similarity=1.340 Sum_probs=5.7
Q ss_pred CCCcccchhHH
Q psy8832 114 NGEPVCNACGL 124 (144)
Q Consensus 114 ~g~~lCnaCgl 124 (144)
.|+.+|..||+
T Consensus 18 ~ge~VC~~CG~ 28 (285)
T COG1405 18 RGEIVCADCGL 28 (285)
T ss_pred CCeEEeccCCE
Confidence 44555555543
No 95
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=34.27 E-value=19 Score=21.13 Aligned_cols=27 Identities=19% Similarity=0.390 Sum_probs=16.3
Q ss_pred cccccCCCCCCCeeeeCCCCCccccccccc
Q psy8832 38 KECVNCAANSTPLWRRDGTGHHLCNACGLY 67 (144)
Q Consensus 38 ~~C~~C~t~~tp~wrr~~~g~~lCnaCgly 67 (144)
-.|.+||+..+-. ...+...|..||-.
T Consensus 4 y~C~~CG~~~~~~---~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 4 YKCARCGREVELD---EYGTGVRCPYCGYR 30 (46)
T ss_pred EECCCCCCEEEEC---CCCCceECCCCCCe
Confidence 4688888754331 11225788888864
No 96
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=34.18 E-value=29 Score=33.94 Aligned_cols=29 Identities=21% Similarity=0.485 Sum_probs=18.9
Q ss_pred CCCCcccccCCCCCCCeeeeCCCCCc--ccccccc
Q psy8832 34 NMDIKECVNCAANSTPLWRRDGTGHH--LCNACGL 66 (144)
Q Consensus 34 ~~~~~~C~~C~t~~tp~wrr~~~g~~--lCnaCgl 66 (144)
+....+|..||-.... +.+|++ -||+||.
T Consensus 14 ~~~~qiCqICGD~vg~----~~~Ge~FVAC~eC~F 44 (1079)
T PLN02638 14 HGGGQVCQICGDNVGK----TVDGEPFVACDVCAF 44 (1079)
T ss_pred ccCCceeeecccccCc----CCCCCEEEEeccCCC
Confidence 3455689999976554 356653 6777665
No 97
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=33.43 E-value=44 Score=30.87 Aligned_cols=46 Identities=26% Similarity=0.622 Sum_probs=28.0
Q ss_pred CCCCCcccccCCCCCCCeeeeCCCCCcccccccccccccCCCCCCccccchhhhhhcCCCCCCcccccCCcccccccc
Q psy8832 33 LNMDIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVNRPPVRTNQKKALQQTGNKRSGVSCANCSTTCTTLWR 110 (144)
Q Consensus 33 ~~~~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~g~~RP~~k~kkkka~~~s~~k~~~~~C~nC~t~~t~~WR 110 (144)
.....+.|.+||+.-+. ..|..||-- + | ....-|.+||+.-.+.|.
T Consensus 11 n~~~akFC~~CG~~l~~---------~~Cp~CG~~------~-~----------------~~~~fC~~CG~~~~~~~~ 56 (645)
T PRK14559 11 NPNNNRFCQKCGTSLTH---------KPCPQCGTE------V-P----------------VDEAHCPNCGAETGTIWW 56 (645)
T ss_pred CCCCCccccccCCCCCC---------CcCCCCCCC------C-C----------------cccccccccCCcccchhh
Confidence 34567789999876432 357777761 1 0 122367777777777774
No 98
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=33.08 E-value=32 Score=18.64 Aligned_cols=27 Identities=30% Similarity=0.669 Sum_probs=13.1
Q ss_pred CcccccCCCCCCCeeeeCCCC-Cccccccccc
Q psy8832 37 IKECVNCAANSTPLWRRDGTG-HHLCNACGLY 67 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr~~~g-~~lCnaCgly 67 (144)
.+-|..||+...+ .+.| ...|.+||..
T Consensus 3 ~rfC~~CG~~t~~----~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKP----APGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-----SSSS-EEESSSS-E
T ss_pred CcccCcCCccccC----CCCcCEeECCCCcCE
Confidence 3568888855443 2334 4688888863
No 99
>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=32.91 E-value=30 Score=24.00 Aligned_cols=31 Identities=26% Similarity=0.619 Sum_probs=20.7
Q ss_pred cccccCCcccccccccCCCCCcccchhHHHHHhhC
Q psy8832 96 VSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHN 130 (144)
Q Consensus 96 ~~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~ 130 (144)
..|.-|+...+- .+ -|-..|+||..+|++.-
T Consensus 5 ~~C~VCg~~a~g-~h---yGv~sC~aCk~FFRR~v 35 (97)
T cd07170 5 RLCLVCGDIASG-YH---YGVASCEACKAFFKRTI 35 (97)
T ss_pred CCCeecCCcCcc-eE---ECceeehhhhHHHHHHh
Confidence 468888763322 11 34567999999998863
No 100
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=32.86 E-value=28 Score=22.65 Aligned_cols=16 Identities=25% Similarity=0.389 Sum_probs=11.5
Q ss_pred CcccccCCCCC-CCeee
Q psy8832 37 IKECVNCAANS-TPLWR 52 (144)
Q Consensus 37 ~~~C~~C~t~~-tp~wr 52 (144)
...|.+||+++ |+.|.
T Consensus 17 ~~~Cp~Cgs~~~S~~w~ 33 (64)
T PRK06393 17 EKTCPVHGDEKTTTEWF 33 (64)
T ss_pred CCcCCCCCCCcCCcCcc
Confidence 34799999887 55665
No 101
>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=32.70 E-value=33 Score=22.98 Aligned_cols=31 Identities=29% Similarity=0.541 Sum_probs=20.9
Q ss_pred cccccCCcccccccccCCCCCcccchhHHHHHhhC
Q psy8832 96 VSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHN 130 (144)
Q Consensus 96 ~~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~ 130 (144)
..|.-|+...+-. .-|-..|+||..+|+++-
T Consensus 4 ~~C~VCg~~~~g~----hyGv~sC~aC~~FFRR~v 34 (82)
T cd07171 4 HFCAVCSDYASGY----HYGVWSCEGCKAFFKRSI 34 (82)
T ss_pred CCCeecCCcCcce----EECceeehhhHHhHHHHe
Confidence 3578887643322 124567999999999874
No 102
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=32.58 E-value=44 Score=18.62 Aligned_cols=29 Identities=24% Similarity=0.563 Sum_probs=17.4
Q ss_pred CcccccCCCCCCCeeeeCCCCCcccccccccc
Q psy8832 37 IKECVNCAANSTPLWRRDGTGHHLCNACGLYN 68 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~ 68 (144)
...|..|+..- -.-..++..+|..||.-+
T Consensus 3 ~~~C~~C~~~~---i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNG---IVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCe---EEEecCCeEEcccCCcEe
Confidence 35677787433 222455556888887643
No 103
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=31.57 E-value=34 Score=26.73 Aligned_cols=30 Identities=27% Similarity=0.710 Sum_probs=24.0
Q ss_pred CCcccccCCCCCCCeeeeCCCCCccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACG 65 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCg 65 (144)
....|..||+.....+-.-..|..+|..|+
T Consensus 148 ~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 148 DLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred chhhHhcCCCCCCceEEecccCCccccccc
Confidence 345899999887766666678889999997
No 104
>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=31.07 E-value=35 Score=22.86 Aligned_cols=31 Identities=23% Similarity=0.643 Sum_probs=20.9
Q ss_pred cccccCCcccccccccCCCCCcccchhHHHHHhhC
Q psy8832 96 VSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHN 130 (144)
Q Consensus 96 ~~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~ 130 (144)
..|.-|+...+-. .-|-..|+||..+|++.-
T Consensus 4 ~~C~VCg~~a~g~----hyGv~sC~aCk~FFRR~v 34 (82)
T cd07173 4 KTCLICGDEASGC----HYGALTCGSCKVFFKRAA 34 (82)
T ss_pred CCCeecCCcCcce----EECcchhhhHHHHHHHHh
Confidence 3588887643322 124566999999999873
No 105
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=30.61 E-value=13 Score=26.44 Aligned_cols=31 Identities=32% Similarity=0.791 Sum_probs=22.3
Q ss_pred ccccCCccccc---ccccCCCCCcccchhHHHHH
Q psy8832 97 SCANCSTTCTT---LWRRNNNGEPVCNACGLYFK 127 (144)
Q Consensus 97 ~C~nC~t~~t~---~WR~~~~g~~lCnaCglyy~ 127 (144)
.|..|+..... +-..+.-|-..|..||++|-
T Consensus 24 tCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 24 TCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred ecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 58888766544 66666666777999999763
No 106
>KOG1597|consensus
Probab=30.50 E-value=40 Score=28.32 Aligned_cols=29 Identities=28% Similarity=0.778 Sum_probs=19.0
Q ss_pred ccccCCCCCCCeeeeCCCCCccccccccc
Q psy8832 39 ECVNCAANSTPLWRRDGTGHHLCNACGLY 67 (144)
Q Consensus 39 ~C~~C~t~~tp~wrr~~~g~~lCnaCgly 67 (144)
.|+.|......+--.-..|.++|-.|||-
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlV 30 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTVCSECGLV 30 (308)
T ss_pred CCCCCCCCCCCeeeeccCCceecccCCee
Confidence 46677655444555566677788888874
No 107
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=30.30 E-value=21 Score=21.97 Aligned_cols=41 Identities=20% Similarity=0.266 Sum_probs=26.7
Q ss_pred ccccCCcccccccccCCCCCcccchhHHHHHhhCCCCccccccccc
Q psy8832 97 SCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHNVFTILFYNITKA 142 (144)
Q Consensus 97 ~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~~~Rp~~l~~~~~ 142 (144)
.|+.|+.....+ ......-|--||- +--=+.||..+|+-||
T Consensus 8 ~C~~Cg~~~~~~---~~~~~irCp~Cg~--rIl~K~R~~~~krvkA 48 (49)
T COG1996 8 KCARCGREVELD---QETRGIRCPYCGS--RILVKERPKVPKRVKA 48 (49)
T ss_pred EhhhcCCeeehh---hccCceeCCCCCc--EEEEeccCCccEEEec
Confidence 689998877433 1223566988885 2223778888887665
No 108
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=30.09 E-value=36 Score=18.00 Aligned_cols=7 Identities=43% Similarity=1.421 Sum_probs=3.1
Q ss_pred ccccccc
Q psy8832 60 LCNACGL 66 (144)
Q Consensus 60 lCnaCgl 66 (144)
.|..||.
T Consensus 16 ~Cp~CG~ 22 (26)
T PF10571_consen 16 FCPHCGY 22 (26)
T ss_pred cCCCCCC
Confidence 4444443
No 109
>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=29.43 E-value=35 Score=21.66 Aligned_cols=29 Identities=28% Similarity=0.772 Sum_probs=19.5
Q ss_pred ccccCCcccccccccCCCCCcccchhHHHHHhh
Q psy8832 97 SCANCSTTCTTLWRRNNNGEPVCNACGLYFKLH 129 (144)
Q Consensus 97 ~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~ 129 (144)
.|.-|+... +.. .-|...|++|..+|+..
T Consensus 2 ~C~VCg~~~-~~~---~ygv~sC~~C~~FFrR~ 30 (70)
T PF00105_consen 2 KCKVCGDPA-SGY---HYGVLSCNACKMFFRRS 30 (70)
T ss_dssp BSTTTSSBE-SEE---ETTEEEEHHHHHHHHHH
T ss_pred CCeECCCcc-Ccc---cccccccccceeeeeec
Confidence 467777532 221 24567899999999886
No 110
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=28.34 E-value=39 Score=23.34 Aligned_cols=33 Identities=24% Similarity=0.379 Sum_probs=26.8
Q ss_pred CCcccccCCCCCCCeeeeCCCCCccccccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRIN 71 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~ 71 (144)
....|..|+.+ .-+|...|-..|+-||.-+...
T Consensus 34 ~~~~Cp~C~~~---~VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRT---TVKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCc---ceeeeccCeEEcCCCCCeeccc
Confidence 56789999965 6688999999999999866543
No 111
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=28.15 E-value=49 Score=33.02 Aligned_cols=22 Identities=23% Similarity=0.671 Sum_probs=14.4
Q ss_pred CcccccCCCCCCCeeeeCCCCCccccccccc
Q psy8832 37 IKECVNCAANSTPLWRRDGTGHHLCNACGLY 67 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly 67 (144)
.+.|.+||+.. +. ..|..||-.
T Consensus 667 ~rkCPkCG~~t-~~--------~fCP~CGs~ 688 (1337)
T PRK14714 667 RRRCPSCGTET-YE--------NRCPDCGTH 688 (1337)
T ss_pred EEECCCCCCcc-cc--------ccCcccCCc
Confidence 47899999743 22 277777763
No 112
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=27.63 E-value=57 Score=20.87 Aligned_cols=27 Identities=26% Similarity=0.688 Sum_probs=14.1
Q ss_pred CcccccCCCCCCCeeeeCCCCCcccccccc
Q psy8832 37 IKECVNCAANSTPLWRRDGTGHHLCNACGL 66 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr~~~g~~lCnaCgl 66 (144)
...|..||..-.|. +..-.+.|..||-
T Consensus 7 ~~~CtSCg~~i~~~---~~~~~F~CPnCG~ 33 (59)
T PRK14890 7 PPKCTSCGIEIAPR---EKAVKFLCPNCGE 33 (59)
T ss_pred CccccCCCCcccCC---CccCEeeCCCCCC
Confidence 34566666555542 2222456666654
No 113
>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=26.83 E-value=44 Score=22.51 Aligned_cols=29 Identities=21% Similarity=0.540 Sum_probs=18.1
Q ss_pred cccCCcccccccccCCCCCcccchhHHHHHhhC
Q psy8832 98 CANCSTTCTTLWRRNNNGEPVCNACGLYFKLHN 130 (144)
Q Consensus 98 C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~ 130 (144)
|.-|+...+-. .-|-..|+||..+|+++-
T Consensus 2 C~VCg~~~~g~----hygv~sC~aC~~FFRR~v 30 (87)
T cd07162 2 CRVCGDRATGY----HFNAMTCEGCKGFFRRAM 30 (87)
T ss_pred CcccCCcCcce----EECcceehhhHHHHHhhh
Confidence 55666532222 123566999999999864
No 114
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=26.73 E-value=39 Score=28.94 Aligned_cols=60 Identities=18% Similarity=0.436 Sum_probs=35.8
Q ss_pred CCCcccccCCCCCCCeeeeCCCCCcccccccccccccCCCCCCccccchhhhhhcCCCCCCcccccCCccccc-ccccCC
Q psy8832 35 MDIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVNRPPVRTNQKKALQQTGNKRSGVSCANCSTTCTT-LWRRNN 113 (144)
Q Consensus 35 ~~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~g~~RP~~k~kkkka~~~s~~k~~~~~C~nC~t~~t~-~WR~~~ 113 (144)
.....|..||.+.-| ..+-||..|++- ..|....+.. -.-..|.+|+....+ .|=..+
T Consensus 4 ~~~~~C~~CGr~~~~------~~~~lC~dC~~~------~~~~~~ip~~---------~~v~~C~~Cga~~~~~~W~~~~ 62 (355)
T COG1499 4 ASTILCVRCGRSVDP------LIDGLCGDCYVE------TTPLIEIPDE---------VNVEVCRHCGAYRIRGRWVDEE 62 (355)
T ss_pred CcccEeccCCCcCch------hhccccHHHHhc------cCccccCCCc---------eEEEECCcCCCccCCCcceecc
Confidence 345689999987653 234599999883 2232222110 112479999966655 676544
Q ss_pred CC
Q psy8832 114 NG 115 (144)
Q Consensus 114 ~g 115 (144)
.+
T Consensus 63 ~~ 64 (355)
T COG1499 63 GA 64 (355)
T ss_pred cc
Confidence 33
No 115
>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=26.66 E-value=24 Score=24.98 Aligned_cols=33 Identities=18% Similarity=0.447 Sum_probs=20.8
Q ss_pred CCcccccCCcccccccccCCCCCcccchhHHHHHhhC
Q psy8832 94 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHN 130 (144)
Q Consensus 94 ~~~~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~ 130 (144)
....|.-|+...+-. .-|-..|+||..+|+++-
T Consensus 5 ~~~~C~VCg~~a~g~----hyGv~sC~aCk~FFRR~v 37 (107)
T cd06955 5 VPRICGVCGDRATGF----HFNAMTCEGCKGFFRRSM 37 (107)
T ss_pred CCCCCeecCCcCccc----EECcceeeeecceeccee
Confidence 345688887643322 123456999998888764
No 116
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=26.61 E-value=40 Score=27.98 Aligned_cols=28 Identities=25% Similarity=0.643 Sum_probs=20.9
Q ss_pred CCcccccCCCCCCCeeeeCCCC-Cccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTG-HHLCNACGLY 67 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g-~~lCnaCgly 67 (144)
.-+-|..||+...+. ..| ...|+.||..
T Consensus 110 ~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~ 138 (279)
T COG2816 110 SHRFCGRCGTKTYPR----EGGWARVCPKCGHE 138 (279)
T ss_pred hCcCCCCCCCcCccc----cCceeeeCCCCCCc
Confidence 468899999887773 222 4799999884
No 117
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=26.17 E-value=33 Score=26.76 Aligned_cols=30 Identities=27% Similarity=0.721 Sum_probs=23.7
Q ss_pred ccccCCCCCCCeeeeCCCCC---cccccccccc
Q psy8832 39 ECVNCAANSTPLWRRDGTGH---HLCNACGLYN 68 (144)
Q Consensus 39 ~C~~C~t~~tp~wrr~~~g~---~lCnaCgly~ 68 (144)
.|.+||.....++++-.+|. ..|..|+-.-
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~va 34 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVA 34 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccCCcc
Confidence 69999999888898865553 5899998743
No 118
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=26.11 E-value=33 Score=19.70 Aligned_cols=31 Identities=32% Similarity=0.675 Sum_probs=18.4
Q ss_pred CcccccCCCCCCCeeeeCCCC-Cccccccccc
Q psy8832 37 IKECVNCAANSTPLWRRDGTG-HHLCNACGLY 67 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr~~~g-~~lCnaCgly 67 (144)
...|.+|++=--|.-.-+..| ...|+-|+..
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 356999999888877777766 5699999873
No 119
>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=25.56 E-value=42 Score=21.82 Aligned_cols=16 Identities=31% Similarity=0.825 Sum_probs=12.8
Q ss_pred CCcccchhHHHHHhhC
Q psy8832 115 GEPVCNACGLYFKLHN 130 (144)
Q Consensus 115 g~~lCnaCglyy~~~~ 130 (144)
|-..|+||..+|+++-
T Consensus 14 gv~sC~aCk~FFRR~~ 29 (73)
T cd06963 14 GVLTCGSCKVFFKRAA 29 (73)
T ss_pred CceeehhhhHhHHHhh
Confidence 4556999999998874
No 120
>KOG1729|consensus
Probab=25.48 E-value=61 Score=26.96 Aligned_cols=22 Identities=27% Similarity=0.576 Sum_probs=16.0
Q ss_pred cCCCCCcccccCCCCCCCe-eee
Q psy8832 32 MLNMDIKECVNCAANSTPL-WRR 53 (144)
Q Consensus 32 ~~~~~~~~C~~C~t~~tp~-wrr 53 (144)
.++....+|..|+.+...+ |||
T Consensus 163 ~PD~ea~~C~~C~~~~Ftl~~RR 185 (288)
T KOG1729|consen 163 LPDSEATECMVCGCTEFTLSERR 185 (288)
T ss_pred cCcccceecccCCCccccHHHHH
Confidence 3567888999999965554 454
No 121
>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=25.28 E-value=44 Score=21.82 Aligned_cols=15 Identities=40% Similarity=0.906 Sum_probs=12.5
Q ss_pred CCcccchhHHHHHhh
Q psy8832 115 GEPVCNACGLYFKLH 129 (144)
Q Consensus 115 g~~lCnaCglyy~~~ 129 (144)
|...|+||..+|++.
T Consensus 14 gv~sC~aCk~FFRR~ 28 (75)
T cd07155 14 GVASCEACKAFFKRT 28 (75)
T ss_pred ChhhhhhhHHHHHHH
Confidence 456799999999886
No 122
>PLN02189 cellulose synthase
Probab=24.60 E-value=53 Score=32.09 Aligned_cols=29 Identities=31% Similarity=0.651 Sum_probs=18.0
Q ss_pred CCCCcccccCCCCCCCeeeeCCCCCc--ccccccc
Q psy8832 34 NMDIKECVNCAANSTPLWRRDGTGHH--LCNACGL 66 (144)
Q Consensus 34 ~~~~~~C~~C~t~~tp~wrr~~~g~~--lCnaCgl 66 (144)
+....+|..||-.... +.+|++ -||+|+.
T Consensus 31 ~~~~~~C~iCgd~vg~----~~~g~~fvaC~~C~f 61 (1040)
T PLN02189 31 NLDGQVCEICGDEIGL----TVDGDLFVACNECGF 61 (1040)
T ss_pred cccCccccccccccCc----CCCCCEEEeeccCCC
Confidence 3345589999976544 355543 6666655
No 123
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.59 E-value=45 Score=26.49 Aligned_cols=26 Identities=23% Similarity=0.488 Sum_probs=18.8
Q ss_pred CCCCcccccCCCCCCCeeeeCCCCCccccccccc
Q psy8832 34 NMDIKECVNCAANSTPLWRRDGTGHHLCNACGLY 67 (144)
Q Consensus 34 ~~~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly 67 (144)
...+..|+.||. -..+...|..||..
T Consensus 306 ~~tS~~C~~cg~--------~~~r~~~C~~cg~~ 331 (364)
T COG0675 306 YYTSKTCPCCGH--------LSGRLFKCPRCGFV 331 (364)
T ss_pred CCCcccccccCC--------ccceeEECCCCCCe
Confidence 345678999998 11335799999984
No 124
>KOG1194|consensus
Probab=24.21 E-value=14 Score=32.86 Aligned_cols=42 Identities=24% Similarity=0.361 Sum_probs=30.8
Q ss_pred ccccCCcccccccccCCCCCcccchhHHHHHhhCCCCccccc
Q psy8832 97 SCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHNVFTILFYN 138 (144)
Q Consensus 97 ~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~~~Rp~~l~ 138 (144)
.=.||+...--+--+....+.-|-+|.+||+.-+++||.+|+
T Consensus 264 ~~~n~~~~~d~~~~~~a~~~~ec~~c~~yf~~~~vpRp~slr 305 (534)
T KOG1194|consen 264 VPSNCGAKSDLLILNRAMSRHECKPCILYFRLMRVPRPASLR 305 (534)
T ss_pred ccccCcchhhHHHHhhhhhccCccCceeeeeccCCCChhHHH
Confidence 334787766554333333467899999999999999998875
No 125
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=24.17 E-value=45 Score=20.70 Aligned_cols=34 Identities=18% Similarity=0.271 Sum_probs=21.6
Q ss_pred CCCCCcccccCCCCCCCeeeeCCCC-Ccccccccc
Q psy8832 33 LNMDIKECVNCAANSTPLWRRDGTG-HHLCNACGL 66 (144)
Q Consensus 33 ~~~~~~~C~~C~t~~tp~wrr~~~g-~~lCnaCgl 66 (144)
.+.-+.+|.+|..-..-.-...... ++.|-.||.
T Consensus 18 ~~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 18 SNRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred cCceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 4556788999997665443333322 567887775
No 126
>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=23.92 E-value=48 Score=21.43 Aligned_cols=16 Identities=25% Similarity=0.646 Sum_probs=12.8
Q ss_pred CCcccchhHHHHHhhC
Q psy8832 115 GEPVCNACGLYFKLHN 130 (144)
Q Consensus 115 g~~lCnaCglyy~~~~ 130 (144)
|-..|+||..+|++.-
T Consensus 14 Gv~~C~aC~~FFRR~v 29 (73)
T cd07158 14 GVHSCEGCKGFFRRTI 29 (73)
T ss_pred CcchhhHHHHHHhhhh
Confidence 4567999999999863
No 127
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=23.84 E-value=45 Score=30.60 Aligned_cols=33 Identities=24% Similarity=0.527 Sum_probs=26.7
Q ss_pred CCcccccCCCCCCCeeeeCCCCCccccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLYNR 69 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r 69 (144)
..+.|.+|+... |.|---.-|-++|..|.=.++
T Consensus 22 gNk~CADCgs~~-P~WASiNlGIFICi~CSGIHR 54 (648)
T PLN03119 22 PNRRCINCNSLG-PQYVCTTFWTFVCMACSGIHR 54 (648)
T ss_pred CCCccccCCCCC-CCceeeccceEEeccchhhhc
Confidence 457899999865 999988889999999965444
No 128
>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=23.82 E-value=51 Score=22.61 Aligned_cols=29 Identities=21% Similarity=0.449 Sum_probs=19.7
Q ss_pred ccccCCCCCCCeeeeCCCCCccccccccccccc
Q psy8832 39 ECVNCAANSTPLWRRDGTGHHLCNACGLYNRIN 71 (144)
Q Consensus 39 ~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~ 71 (144)
.|..||...+-. + -|-+.|+||..|++..
T Consensus 2 ~C~VCg~~a~g~-h---yGv~sC~aC~~FFRR~ 30 (94)
T cd06966 2 ICGVCGDKALGY-N---FNAITCESCKAFFRRN 30 (94)
T ss_pred CCeeCCCcCcce-E---ECcceeeeehheehhc
Confidence 588898643332 1 2456899999998753
No 129
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.81 E-value=34 Score=23.15 Aligned_cols=32 Identities=19% Similarity=0.549 Sum_probs=20.2
Q ss_pred ccccCCcccccccccCCCCCcccchhHHHHHh
Q psy8832 97 SCANCSTTCTTLWRRNNNGEPVCNACGLYFKL 128 (144)
Q Consensus 97 ~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~ 128 (144)
.|.+|+....-+..-..+-...|.+|+-..|+
T Consensus 14 ~c~~cg~~~dvvq~~~ddplt~ce~c~a~~kk 45 (82)
T COG2331 14 ECTECGNRFDVVQAMTDDPLTTCEECGARLKK 45 (82)
T ss_pred eecccchHHHHHHhcccCccccChhhChHHHH
Confidence 57778776666544333335678888875554
No 130
>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=23.49 E-value=54 Score=21.33 Aligned_cols=16 Identities=25% Similarity=0.758 Sum_probs=12.9
Q ss_pred CCcccchhHHHHHhhC
Q psy8832 115 GEPVCNACGLYFKLHN 130 (144)
Q Consensus 115 g~~lCnaCglyy~~~~ 130 (144)
|-..|+||..+|+++-
T Consensus 14 gv~sC~aC~~FFRR~~ 29 (74)
T cd07179 14 GALTCEGCKGFFRRTE 29 (74)
T ss_pred CceeehhHHHHHHHHh
Confidence 4556999999999874
No 131
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=23.29 E-value=72 Score=26.62 Aligned_cols=36 Identities=19% Similarity=0.479 Sum_probs=25.2
Q ss_pred CCCCcccccCCCCCCCeee---eCCC-CC---ccccccccccc
Q psy8832 34 NMDIKECVNCAANSTPLWR---RDGT-GH---HLCNACGLYNR 69 (144)
Q Consensus 34 ~~~~~~C~~C~t~~tp~wr---r~~~-g~---~lCnaCgly~r 69 (144)
......|..||-.....|. |+.+ +. +.|..||..|+
T Consensus 255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 255 VTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred CcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 4456789999988877764 3333 32 48999998765
No 132
>KOG2879|consensus
Probab=23.28 E-value=94 Score=25.98 Aligned_cols=57 Identities=19% Similarity=0.303 Sum_probs=37.4
Q ss_pred CCCCCcccccCCCCCCCeeeeCCCCCcccccccccccccCCCCCCccccchhhhhhcCCCCCCcccccCCcccccccc
Q psy8832 33 LNMDIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVNRPPVRTNQKKALQQTGNKRSGVSCANCSTTCTTLWR 110 (144)
Q Consensus 33 ~~~~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~g~~RP~~k~kkkka~~~s~~k~~~~~C~nC~t~~t~~WR 110 (144)
......+|.-||...|--..-++=|+.-|=-|.. .+..-.....|.+|+...-|+-+
T Consensus 235 ~~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~---------------------ts~~~~asf~Cp~Cg~~~~~lq~ 291 (298)
T KOG2879|consen 235 TGTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIA---------------------TSRLWDASFTCPLCGENVEPLQA 291 (298)
T ss_pred cccCCceeeccCCCCCCCeeeccccceeehhhhh---------------------hhhcchhhcccCccCCCCcchhh
Confidence 3456789999999888877766677755444432 11122234578999888877754
No 133
>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=23.12 E-value=65 Score=21.90 Aligned_cols=31 Identities=29% Similarity=0.557 Sum_probs=20.7
Q ss_pred cccccCCcccccccccCCCCCcccchhHHHHHhhC
Q psy8832 96 VSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHN 130 (144)
Q Consensus 96 ~~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~ 130 (144)
..|.-|+...+-.+ -|-..|+||..+|+.+-
T Consensus 7 ~~C~VCg~~a~g~h----yGv~sC~aCk~FFRR~v 37 (90)
T cd07169 7 RTCLICGDRATGLH----YGIISCEGCKGFFKRSI 37 (90)
T ss_pred CCCeecCCcCcceE----ECcceehhhHHHHHHHh
Confidence 45788876433331 24567999999998864
No 134
>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=22.99 E-value=66 Score=22.13 Aligned_cols=31 Identities=19% Similarity=0.650 Sum_probs=20.8
Q ss_pred cccccCCcccccccccCCCCCcccchhHHHHHhhC
Q psy8832 96 VSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHN 130 (144)
Q Consensus 96 ~~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~~ 130 (144)
..|.-|+...+-. + -|-..|+||..+|+++-
T Consensus 6 ~~C~VCg~~~~g~-h---yGv~sC~aC~~FFRR~v 36 (95)
T cd06968 6 IPCKICGDKSSGI-H---YGVITCEGCKGFFRRSQ 36 (95)
T ss_pred cCCcccCCcCcce-E---ECceeehhhHHhhHHhe
Confidence 3588887644333 2 34566999999998864
No 135
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=22.85 E-value=30 Score=19.03 Aligned_cols=24 Identities=29% Similarity=0.646 Sum_probs=10.4
Q ss_pred cccccCCcccccccccCCCCCcccchhH
Q psy8832 96 VSCANCSTTCTTLWRRNNNGEPVCNACG 123 (144)
Q Consensus 96 ~~C~nC~t~~t~~WR~~~~g~~lCnaCg 123 (144)
..|..|+.+.+-. .....+|..|+
T Consensus 3 p~Cp~C~se~~y~----D~~~~vCp~C~ 26 (30)
T PF08274_consen 3 PKCPLCGSEYTYE----DGELLVCPECG 26 (30)
T ss_dssp ---TTT-----EE-----SSSEEETTTT
T ss_pred CCCCCCCCcceec----cCCEEeCCccc
Confidence 3677888777762 23367788886
No 136
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=22.50 E-value=46 Score=19.63 Aligned_cols=30 Identities=27% Similarity=0.574 Sum_probs=18.7
Q ss_pred CCCcccccCCCCCCCeeeeCCCCCcccccccccc
Q psy8832 35 MDIKECVNCAANSTPLWRRDGTGHHLCNACGLYN 68 (144)
Q Consensus 35 ~~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~ 68 (144)
.....|..|+ ..+|-....| +.|..|++..
T Consensus 9 ~~~~~C~~C~---~~i~g~~~~g-~~C~~C~~~~ 38 (53)
T PF00130_consen 9 SKPTYCDVCG---KFIWGLGKQG-YRCSWCGLVC 38 (53)
T ss_dssp SSTEB-TTSS---SBECSSSSCE-EEETTTT-EE
T ss_pred CCCCCCcccC---cccCCCCCCe-EEECCCCChH
Confidence 3455799998 4556644444 7899999854
No 137
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=22.38 E-value=52 Score=26.13 Aligned_cols=31 Identities=16% Similarity=0.322 Sum_probs=22.8
Q ss_pred CCcccccCCCCCCCeeeeCCCCCcccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGL 66 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgl 66 (144)
....|+.||--....--+..+|.++|-.|.-
T Consensus 171 ~~v~C~kCGE~~~e~~~~~~ng~~vC~~C~~ 201 (206)
T COG2191 171 GSVRCSKCGELFMEPRAVVLNGKPVCKPCAE 201 (206)
T ss_pred ceeeccccCcccccchhhhcCCceecccccc
Confidence 3468999996555544456789999999964
No 138
>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=21.94 E-value=75 Score=21.74 Aligned_cols=32 Identities=22% Similarity=0.351 Sum_probs=21.7
Q ss_pred CCcccccCCCCCCCeeeeCCCCCccccccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRIN 71 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~ 71 (144)
+...|..||...+-. --|-..|+||..|++..
T Consensus 5 p~~~C~VCg~~a~g~----hyGv~sC~aCk~FFRR~ 36 (92)
T cd06970 5 PGLLCRVCGDTSSGK----HYGIYACNGCSGFFKRS 36 (92)
T ss_pred CCCCCeecCCcCccc----EECccEEeeeeeEeeee
Confidence 344699999654432 12456899999998754
No 139
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=21.69 E-value=1.2e+02 Score=26.06 Aligned_cols=31 Identities=29% Similarity=0.636 Sum_probs=21.5
Q ss_pred CCCcccccCCcccccccccC-CCCCcccchhHH
Q psy8832 93 RSGVSCANCSTTCTTLWRRN-NNGEPVCNACGL 124 (144)
Q Consensus 93 ~~~~~C~nC~t~~t~~WR~~-~~g~~lCnaCgl 124 (144)
..-..|.| .....--|--- ++++.+|-||.+
T Consensus 51 ~~~~~C~N-~~~~~CNWlvp~~~~~~~C~aCrl 82 (343)
T PF10005_consen 51 RRYRRCAN-AEHAVCNWLVPADDPDALCRACRL 82 (343)
T ss_pred ceeeeCCC-CCccccceeecCCCCCCcchhhhc
Confidence 34467999 66666778643 334689999976
No 140
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=21.65 E-value=49 Score=30.36 Aligned_cols=36 Identities=19% Similarity=0.305 Sum_probs=28.1
Q ss_pred CCCcccccCCcccccccccCCCCCcccchhHHHHHhh
Q psy8832 93 RSGVSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLH 129 (144)
Q Consensus 93 ~~~~~C~nC~t~~t~~WR~~~~g~~lCnaCglyy~~~ 129 (144)
.-+..|.+|+... |.|---+-|-.||-.|.=.-|..
T Consensus 21 PgNk~CADCgs~~-P~WASiNlGIFICi~CSGIHRsL 56 (648)
T PLN03119 21 PPNRRCINCNSLG-PQYVCTTFWTFVCMACSGIHREF 56 (648)
T ss_pred cCCCccccCCCCC-CCceeeccceEEeccchhhhccC
Confidence 3457899999865 99988888999999997544433
No 141
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=21.04 E-value=59 Score=19.86 Aligned_cols=27 Identities=22% Similarity=0.487 Sum_probs=18.1
Q ss_pred cccCCccccccc-ccCCCCCcccchhHHH
Q psy8832 98 CANCSTTCTTLW-RRNNNGEPVCNACGLY 125 (144)
Q Consensus 98 C~nC~t~~t~~W-R~~~~g~~lCnaCgly 125 (144)
|.-|+....-+- .+-.+| .||..|.-.
T Consensus 2 C~iCg~kigl~~~~k~~DG-~iC~~C~~K 29 (51)
T PF14471_consen 2 CAICGKKIGLFKRFKIKDG-YICKDCLKK 29 (51)
T ss_pred CCccccccccccceeccCc-cchHHHHHH
Confidence 666776666554 345666 799999753
No 142
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=20.88 E-value=48 Score=20.88 Aligned_cols=24 Identities=25% Similarity=0.757 Sum_probs=15.0
Q ss_pred CCCcccccCCCCCCCeeeeCCCCCccccccccc
Q psy8832 35 MDIKECVNCAANSTPLWRRDGTGHHLCNACGLY 67 (144)
Q Consensus 35 ~~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly 67 (144)
+..+.|.+||+.+. ...|..||--
T Consensus 3 s~mr~C~~CgvYTL---------k~~CP~CG~~ 26 (56)
T PRK13130 3 SKIRKCPKCGVYTL---------KEICPVCGGK 26 (56)
T ss_pred ccceECCCCCCEEc---------cccCcCCCCC
Confidence 34567888886554 1367777753
No 143
>PLN03131 hypothetical protein; Provisional
Probab=20.77 E-value=57 Score=30.24 Aligned_cols=33 Identities=21% Similarity=0.514 Sum_probs=26.5
Q ss_pred CCcccccCCCCCCCeeeeCCCCCccccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLYNR 69 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r 69 (144)
....|.+|+.. -|.|---.-|-++|..|.=.++
T Consensus 22 gNk~CADCga~-~P~WASiNlGIFICi~CSGIHR 54 (705)
T PLN03131 22 PNRRCINCNSL-GPQFVCTNFWTFICMTCSGIHR 54 (705)
T ss_pred CCCccccCCCC-CCCeeEeccceEEchhchhhhc
Confidence 45689999975 5999988889999999965444
No 144
>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=20.67 E-value=70 Score=21.58 Aligned_cols=31 Identities=19% Similarity=0.517 Sum_probs=21.2
Q ss_pred CcccccCCCCCCCeeeeCCCCCccccccccccccc
Q psy8832 37 IKECVNCAANSTPLWRRDGTGHHLCNACGLYNRIN 71 (144)
Q Consensus 37 ~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly~r~~ 71 (144)
...|..||...+-. + -|-..|+||..+++..
T Consensus 3 ~~~C~VCg~~~~g~-h---yGv~sC~aC~~FFRR~ 33 (87)
T cd06967 3 VELCVVCGDKASGR-H---YGAVSCEGCKGFFKRS 33 (87)
T ss_pred CCCCeecCCcCCcC-E---eCcceEeeeeeEeeee
Confidence 34599999644432 2 3456899999998753
No 145
>COG3952 Predicted membrane protein [Function unknown]
Probab=20.50 E-value=26 Score=25.15 Aligned_cols=21 Identities=29% Similarity=0.547 Sum_probs=13.9
Q ss_pred ccccCCCCCcccchhHHHHHhh
Q psy8832 108 LWRRNNNGEPVCNACGLYFKLH 129 (144)
Q Consensus 108 ~WR~~~~g~~lCnaCglyy~~~ 129 (144)
+||.++- ..+|++||++-...
T Consensus 76 i~~~DpV-~Vl~~~~glF~~l~ 96 (113)
T COG3952 76 IRRQDPV-FVLGQACGLFIYLR 96 (113)
T ss_pred HHhcchH-HHHHHhhhHHHHHH
Confidence 3554444 48899999975443
No 146
>PHA02942 putative transposase; Provisional
Probab=20.28 E-value=79 Score=27.11 Aligned_cols=28 Identities=18% Similarity=0.509 Sum_probs=19.7
Q ss_pred CCcccccCCCCCCCeeeeCCCCCccccccccc
Q psy8832 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGLY 67 (144)
Q Consensus 36 ~~~~C~~C~t~~tp~wrr~~~g~~lCnaCgly 67 (144)
.+..|+.||....++ ....+.|..||..
T Consensus 324 TSq~Cs~CG~~~~~l----~~r~f~C~~CG~~ 351 (383)
T PHA02942 324 SSVSCPKCGHKMVEI----AHRYFHCPSCGYE 351 (383)
T ss_pred CCccCCCCCCccCcC----CCCEEECCCCCCE
Confidence 567899999765422 2235799999985
Done!