Query 033547
Match_columns 117
No_of_seqs 169 out of 816
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 03:32:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033547.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033547hhsearch_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 9.2E-19 2E-23 111.2 3.2 49 16-64 1-50 (54)
2 smart00401 ZnF_GATA zinc finge 99.7 1.4E-17 3E-22 104.9 3.0 48 13-60 2-50 (52)
3 PF00320 GATA: GATA zinc finge 99.6 1.2E-16 2.5E-21 93.9 1.6 35 17-51 1-35 (36)
4 KOG1601 GATA-4/5/6 transcripti 99.0 1.4E-10 3E-15 86.1 2.7 53 14-66 199-251 (340)
5 COG5641 GAT1 GATA Zn-finger-co 98.9 1E-09 2.2E-14 95.4 2.5 54 13-67 157-216 (498)
6 KOG3554 Histone deacetylase co 93.8 0.053 1.1E-06 48.3 2.9 37 14-50 386-424 (693)
7 COG5641 GAT1 GATA Zn-finger-co 91.3 0.095 2.1E-06 46.2 1.2 51 14-64 297-348 (498)
8 PF14803 Nudix_N_2: Nudix N-te 84.8 0.19 4.1E-06 29.1 -0.7 30 15-44 1-30 (34)
9 PF01412 ArfGap: Putative GTPa 83.4 1.2 2.7E-05 31.4 2.8 37 12-50 11-47 (116)
10 smart00105 ArfGap Putative GTP 81.5 1.7 3.6E-05 30.6 2.8 45 13-59 2-50 (112)
11 PRK03988 translation initiatio 79.4 0.48 1.1E-05 35.2 -0.5 29 15-44 103-131 (138)
12 smart00653 eIF2B_5 domain pres 78.5 0.57 1.2E-05 33.5 -0.3 29 15-44 81-109 (110)
13 TIGR00311 aIF-2beta translatio 77.7 0.59 1.3E-05 34.5 -0.5 29 15-44 98-126 (133)
14 COG5347 GTPase-activating prot 74.1 1.6 3.4E-05 36.6 1.1 32 11-44 17-48 (319)
15 PRK12336 translation initiatio 73.8 0.85 1.8E-05 35.5 -0.5 29 15-44 99-127 (201)
16 KOG3740 Uncharacterized conser 71.4 2.3 5E-05 39.0 1.5 38 11-48 459-499 (706)
17 PF13248 zf-ribbon_3: zinc-rib 71.3 2.6 5.6E-05 22.5 1.2 23 14-44 2-24 (26)
18 PF08271 TF_Zn_Ribbon: TFIIB z 70.4 1.5 3.2E-05 25.8 0.1 26 16-44 2-27 (43)
19 PF01873 eIF-5_eIF-2B: Domain 68.3 1.3 2.8E-05 32.3 -0.6 28 15-43 94-121 (125)
20 PLN03119 putative ADP-ribosyla 68.1 2.7 5.8E-05 38.3 1.3 45 13-59 22-67 (648)
21 PLN03114 ADP-ribosylation fact 66.1 4.6 0.0001 34.9 2.2 45 13-59 21-69 (395)
22 PLN03131 hypothetical protein; 63.2 4.1 8.9E-05 37.4 1.5 45 13-59 22-67 (705)
23 PRK12286 rpmF 50S ribosomal pr 63.0 1.8 4E-05 27.6 -0.5 23 14-45 27-49 (57)
24 PF15396 FAM60A: Protein Famil 60.8 5.7 0.00012 31.8 1.7 22 37-59 50-71 (213)
25 COG3529 Predicted nucleic-acid 59.8 2 4.4E-05 28.4 -0.8 34 14-47 10-43 (66)
26 PF06677 Auto_anti-p27: Sjogre 59.4 3.1 6.7E-05 25.0 0.0 25 14-43 17-41 (41)
27 PRK14892 putative transcriptio 58.2 2.4 5.2E-05 30.0 -0.7 35 14-49 21-55 (99)
28 KOG0703 Predicted GTPase-activ 56.7 4.2 9E-05 33.8 0.4 27 14-42 25-51 (287)
29 KOG1598 Transcription initiati 55.6 6.2 0.00013 35.3 1.3 42 15-59 1-42 (521)
30 PF11781 RRN7: RNA polymerase 54.8 5.1 0.00011 23.3 0.4 27 13-44 7-33 (36)
31 PF09889 DUF2116: Uncharacteri 54.0 11 0.00024 24.3 1.9 29 13-49 2-31 (59)
32 smart00778 Prim_Zn_Ribbon Zinc 53.7 6.9 0.00015 23.0 0.9 29 14-43 3-32 (37)
33 PRK00423 tfb transcription ini 53.6 5.7 0.00012 32.5 0.7 31 13-46 10-40 (310)
34 PF13240 zinc_ribbon_2: zinc-r 53.1 8 0.00017 20.3 1.0 20 17-44 2-21 (23)
35 PF09297 zf-NADH-PPase: NADH p 53.1 2.3 4.9E-05 23.6 -1.2 27 14-44 3-29 (32)
36 COG2816 NPY1 NTP pyrophosphohy 53.0 4.4 9.5E-05 33.6 -0.1 34 12-49 109-142 (279)
37 PF09526 DUF2387: Probable met 52.5 3.1 6.7E-05 27.7 -0.9 35 14-48 8-42 (71)
38 PF07282 OrfB_Zn_ribbon: Putat 48.3 8.4 0.00018 24.2 0.7 29 13-45 27-55 (69)
39 PRK00420 hypothetical protein; 47.5 7.5 0.00016 28.1 0.4 29 14-47 23-51 (112)
40 PF02701 zf-Dof: Dof domain, z 47.1 32 0.0007 22.7 3.3 44 12-55 3-49 (63)
41 COG0846 SIR2 NAD-dependent pro 44.5 2.3 4.9E-05 34.4 -2.9 32 14-45 122-155 (250)
42 PRK08351 DNA-directed RNA poly 44.2 12 0.00026 24.4 0.9 16 15-30 16-32 (61)
43 COG3952 Predicted membrane pro 43.3 6.2 0.00013 28.7 -0.6 20 27-48 76-95 (113)
44 PF06689 zf-C4_ClpX: ClpX C4-t 42.9 10 0.00022 22.3 0.4 31 15-46 2-34 (41)
45 KOG3507 DNA-directed RNA polym 42.2 17 0.00037 23.8 1.4 34 11-49 17-50 (62)
46 TIGR02443 conserved hypothetic 41.9 5.8 0.00013 25.8 -0.8 33 14-46 9-41 (59)
47 PF09723 Zn-ribbon_8: Zinc rib 41.3 6.9 0.00015 23.0 -0.5 28 16-44 7-34 (42)
48 PF12773 DZR: Double zinc ribb 41.2 16 0.00034 21.6 1.1 27 13-44 11-37 (50)
49 smart00659 RPOLCX RNA polymera 40.9 8.4 0.00018 23.2 -0.1 29 16-49 4-32 (44)
50 COG4260 Membrane protease subu 40.8 15 0.00032 31.2 1.2 29 13-44 314-342 (345)
51 PF01783 Ribosomal_L32p: Ribos 40.4 4.7 0.0001 25.3 -1.3 21 14-43 26-46 (56)
52 PRK11788 tetratricopeptide rep 39.5 12 0.00026 29.6 0.5 24 13-44 353-376 (389)
53 KOG0706 Predicted GTPase-activ 39.0 14 0.00031 32.6 0.9 37 11-49 20-56 (454)
54 PF10897 DUF2713: Protein of u 38.2 12 0.00026 30.2 0.3 15 103-117 120-134 (246)
55 COG3880 Modulator of heat shoc 37.4 19 0.00041 28.1 1.3 9 98-106 151-160 (176)
56 PRK00085 recO DNA repair prote 36.2 17 0.00036 28.0 0.8 28 15-43 150-177 (247)
57 PF14227 UBN2_2: gag-polypepti 35.7 29 0.00064 23.5 1.9 26 87-112 52-77 (119)
58 PRK06393 rpoE DNA-directed RNA 35.4 23 0.00049 23.3 1.2 17 14-30 17-34 (64)
59 TIGR02605 CxxC_CxxC_SSSS putat 35.3 12 0.00027 22.3 -0.0 29 15-44 6-34 (52)
60 PF12760 Zn_Tnp_IS1595: Transp 35.3 11 0.00025 22.3 -0.2 26 15-43 19-44 (46)
61 PF03604 DNA_RNApol_7kD: DNA d 34.7 16 0.00034 20.8 0.4 25 16-45 2-26 (32)
62 TIGR01031 rpmF_bact ribosomal 34.3 8.7 0.00019 24.2 -0.8 23 14-45 26-48 (55)
63 PF04810 zf-Sec23_Sec24: Sec23 34.1 15 0.00031 21.4 0.1 31 14-44 2-32 (40)
64 TIGR01385 TFSII transcription 33.1 10 0.00022 31.4 -0.8 34 13-47 257-297 (299)
65 KOG1597 Transcription initiati 32.6 18 0.00039 30.5 0.5 33 16-49 2-34 (308)
66 smart00661 RPOL9 RNA polymeras 32.1 21 0.00045 21.1 0.6 27 16-44 2-28 (52)
67 COG1601 GCD7 Translation initi 32.0 14 0.00031 27.9 -0.2 30 14-44 105-134 (151)
68 PRK01110 rpmF 50S ribosomal pr 31.7 13 0.00029 23.8 -0.3 23 14-46 27-49 (60)
69 cd07168 NR_DBD_DHR4_like DNA-b 31.5 41 0.00089 22.9 2.1 33 12-49 4-36 (90)
70 COG1405 SUA7 Transcription ini 30.9 17 0.00036 30.0 0.0 9 36-44 20-28 (285)
71 COG5349 Uncharacterized protei 30.7 15 0.00033 27.2 -0.2 34 13-49 20-53 (126)
72 PF08273 Prim_Zn_Ribbon: Zinc- 30.6 17 0.00037 21.6 0.1 27 15-42 4-32 (40)
73 cd07172 NR_DBD_GR_PR DNA-bindi 30.5 42 0.00091 22.2 1.9 30 15-49 3-32 (78)
74 PF14122 YokU: YokU-like prote 30.2 16 0.00035 25.5 -0.1 33 16-49 1-48 (87)
75 PF07754 DUF1610: Domain of un 29.8 21 0.00046 19.2 0.3 23 17-43 1-23 (24)
76 PF04161 Arv1: Arv1-like famil 29.5 20 0.00044 27.6 0.3 28 16-43 2-31 (208)
77 PHA00626 hypothetical protein 28.8 13 0.00029 24.2 -0.7 33 16-49 2-36 (59)
78 smart00834 CxxC_CXXC_SSSS Puta 28.7 15 0.00033 20.5 -0.4 29 15-44 6-34 (41)
79 PF09610 Myco_arth_vir_N: Myco 28.6 30 0.00065 20.1 0.8 14 102-115 16-29 (33)
80 cd07169 NR_DBD_GCNF_like DNA-b 28.3 54 0.0012 22.3 2.2 32 13-49 5-36 (90)
81 cd07173 NR_DBD_AR DNA-binding 28.0 53 0.0011 22.0 2.1 31 14-49 3-33 (82)
82 TIGR03573 WbuX N-acetyl sugar 28.0 53 0.0011 27.1 2.5 32 14-48 1-33 (343)
83 PF10083 DUF2321: Uncharacteri 27.5 22 0.00048 27.3 0.2 33 14-46 39-78 (158)
84 PF12553 DUF3742: Protein of u 27.3 22 0.00048 22.5 0.2 9 26-34 34-42 (54)
85 cd07170 NR_DBD_ERR DNA-binding 27.3 50 0.0011 22.9 1.9 31 14-49 4-34 (97)
86 PF09947 DUF2180: Uncharacteri 27.2 36 0.00078 22.6 1.2 32 13-44 15-64 (68)
87 PF02591 DUF164: Putative zinc 27.1 14 0.00031 22.7 -0.8 29 14-44 22-54 (56)
88 COG0675 Transposase and inacti 24.5 33 0.00071 26.4 0.7 24 13-45 308-331 (364)
89 PF09698 GSu_C4xC__C2xCH: Geob 24.2 41 0.00089 19.2 0.9 18 22-42 18-35 (36)
90 cd06968 NR_DBD_ROR DNA-binding 23.9 66 0.0014 22.1 2.0 31 14-49 5-35 (95)
91 PHA02998 RNA polymerase subuni 23.9 21 0.00045 28.2 -0.5 36 13-48 142-183 (195)
92 cd07171 NR_DBD_ER DNA-binding 23.8 70 0.0015 21.4 2.1 30 15-49 4-33 (82)
93 cd02337 ZZ_CBP Zinc finger, ZZ 23.6 57 0.0012 19.2 1.5 29 16-44 2-30 (41)
94 PRK00241 nudC NADH pyrophospha 22.8 30 0.00065 27.7 0.1 32 13-48 98-129 (256)
95 PF10058 DUF2296: Predicted in 21.9 35 0.00076 21.4 0.3 36 9-44 17-52 (54)
96 PRK00398 rpoP DNA-directed RNA 21.9 25 0.00053 20.7 -0.4 29 15-47 4-32 (46)
97 cd07158 NR_DBD_Ppar_like The D 21.8 70 0.0015 20.6 1.8 28 17-49 1-28 (73)
98 PF08274 PhnA_Zn_Ribbon: PhnA 21.7 23 0.00049 19.9 -0.5 23 16-43 4-26 (30)
99 smart00440 ZnF_C2C2 C2C2 Zinc 21.4 13 0.00028 21.8 -1.7 31 16-46 2-38 (40)
100 PRK05342 clpX ATP-dependent pr 21.3 81 0.0017 27.0 2.5 29 13-43 8-38 (412)
101 PRK00432 30S ribosomal protein 20.7 25 0.00055 21.6 -0.5 29 12-45 18-46 (50)
102 cd07160 NR_DBD_LXR DNA-binding 20.5 88 0.0019 21.9 2.1 31 14-49 18-48 (101)
103 cd07179 2DBD_NR_DBD2 The secon 20.5 87 0.0019 20.3 2.0 28 17-49 1-28 (74)
104 PF03811 Zn_Tnp_IS1: InsA N-te 20.0 50 0.0011 19.1 0.7 30 12-42 3-35 (36)
105 KOG2767 Translation initiation 20.0 39 0.00085 29.3 0.3 32 15-46 97-128 (400)
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=99.74 E-value=9.2e-19 Score=111.23 Aligned_cols=49 Identities=43% Similarity=0.979 Sum_probs=43.9
Q ss_pred ccccCCCCCCCccccCCCCCCccchHHHHHHHHhcccccCCCCc-chhhh
Q 033547 16 SCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKKLALLGRDK-GRAQK 64 (117)
Q Consensus 16 ~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~~~~rp~~~~~-~~~~~ 64 (117)
.|+||++++||+||+||.+..+|||||||||++++..||..+.. ..+..
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~~~~~~~ 50 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRKKDQIKR 50 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCccccccc
Confidence 59999999999999999888999999999999999999999887 44443
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.69 E-value=1.4e-17 Score=104.90 Aligned_cols=48 Identities=50% Similarity=1.024 Sum_probs=43.2
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHHHHHHhccc-ccCCCCcc
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKKL-ALLGRDKG 60 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~~~~-rp~~~~~~ 60 (117)
....|+||++++||+||+||.|+..|||+|||||+++++. +|..+.+.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~~~ 50 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLKKD 50 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCCCCccccccc
Confidence 4678999999999999999999889999999999999887 88777654
No 3
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.62 E-value=1.2e-16 Score=93.87 Aligned_cols=35 Identities=60% Similarity=1.277 Sum_probs=28.2
Q ss_pred cccCCCCCCCccccCCCCCCccchHHHHHHHHhcc
Q 033547 17 CIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKK 51 (117)
Q Consensus 17 C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~~~ 51 (117)
|++|+|++||+||++|.|+.+|||+|||||+++++
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 89999999999999999977799999999999854
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=99.02 E-value=1.4e-10 Score=86.14 Aligned_cols=53 Identities=47% Similarity=0.986 Sum_probs=47.3
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHHHHHHhcccccCCCCcchhhhhh
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKKLALLGRDKGRAQKRK 66 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~~~~rp~~~~~~~~~~r~ 66 (117)
...|.+|++++||+||+++.|++.+|||||++++++.+.+++......+..+.
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~~ 251 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPRN 251 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCccccccccCccccccc
Confidence 47999999999999999999999999999999999987788887777766654
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.86 E-value=1e-09 Score=95.37 Aligned_cols=54 Identities=31% Similarity=0.680 Sum_probs=50.3
Q ss_pred CCcccccCCCCCCCccccCCC-----CCCccchHHHHHHHHhcccc-cCCCCcchhhhhhh
Q 033547 13 MNKSCIDCHTTRTPLWRGGPA-----GPRSLCNACGIRYRKTKKLA-LLGRDKGRAQKRKR 67 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~-----G~~~lCNaCGl~~~k~~~~r-p~~~~~~~~~~r~r 67 (117)
+..+|.||.|+.||+|||+.. | -++|||||||++-|++.| |+.++...+..+.+
T Consensus 157 ~~~vc~Nc~t~stPlwrR~~~~~s~~~-n~lcnaCgl~~klhg~~r~P~t~ks~~~ks~~~ 216 (498)
T COG5641 157 QPHVCSNCKTTSTPLWRRASSESSLPG-NNLCNACGLYLKLHGSPRAPISLKSDSIKSRSS 216 (498)
T ss_pred ccchhccccccCCccccccccccccCC-ccccccccccccccCCcCCCccccccccccccc
Confidence 556999999999999999998 6 799999999999999999 99999999998885
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=93.79 E-value=0.053 Score=48.25 Aligned_cols=37 Identities=32% Similarity=0.709 Sum_probs=32.5
Q ss_pred CcccccCCCCCCCcc--ccCCCCCCccchHHHHHHHHhc
Q 033547 14 NKSCIDCHTTRTPLW--RGGPAGPRSLCNACGIRYRKTK 50 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~W--R~gp~G~~~lCNaCGl~~~k~~ 50 (117)
.+.|.+|+|++.-+| ..+|+-...||-.|=+||+|.+
T Consensus 386 g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKyg 424 (693)
T KOG3554|consen 386 GRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYG 424 (693)
T ss_pred CCcccccccccccceeccCCCCccchhhHHHHHHHHHhc
Confidence 679999999999999 5566766789999999999985
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=91.27 E-value=0.095 Score=46.24 Aligned_cols=51 Identities=27% Similarity=0.318 Sum_probs=41.3
Q ss_pred CcccccCCC-CCCCccccCCCCCCccchHHHHHHHHhcccccCCCCcchhhh
Q 033547 14 NKSCIDCHT-TRTPLWRGGPAGPRSLCNACGIRYRKTKKLALLGRDKGRAQK 64 (117)
Q Consensus 14 ~~~C~~C~t-t~Tp~WR~gp~G~~~lCNaCGl~~~k~~~~rp~~~~~~~~~~ 64 (117)
...+.+|.+ +.||.||+...---++||+||++.+.++..+|+.-+.+...+
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d~n~~ 348 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPNSK 348 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCCcccccccCCCCChhhh
Confidence 556778877 788999888765579999999999999999998876665555
No 8
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=84.80 E-value=0.19 Score=29.13 Aligned_cols=30 Identities=30% Similarity=0.567 Sum_probs=15.1
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
+.|.+||..-+..-=.|.+-+..+|.+||.
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 469999987433322455666789999983
No 9
>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=83.43 E-value=1.2 Score=31.35 Aligned_cols=37 Identities=32% Similarity=0.547 Sum_probs=25.6
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchHHHHHHHHhc
Q 033547 12 EMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTK 50 (117)
Q Consensus 12 ~~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~~ 50 (117)
...+.|++|+.. -|.|-.-..| -.||-.|.-.++..+
T Consensus 11 ~~N~~CaDCg~~-~p~w~s~~~G-iflC~~Cag~HR~lg 47 (116)
T PF01412_consen 11 PGNKVCADCGAP-NPTWASLNYG-IFLCLECAGIHRSLG 47 (116)
T ss_dssp TTCTB-TTT-SB-S--EEETTTT-EEE-HHHHHHHHHHT
T ss_pred cCcCcCCCCCCC-CCCEEEeecC-hhhhHHHHHHHHHhc
Confidence 356789999954 4599999999 799999987777764
No 10
>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=81.46 E-value=1.7 Score=30.55 Aligned_cols=45 Identities=31% Similarity=0.509 Sum_probs=34.0
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHHHHHHhcc----cccCCCCc
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKK----LALLGRDK 59 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~~~----~rp~~~~~ 59 (117)
....|++|+. .-|.|-.-..| -.+|-.|.-..+..+. .+.+.|+.
T Consensus 2 ~N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~lg~his~VkSl~md~ 50 (112)
T smart00105 2 GNKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRSLGVHISKVRSLTLDT 50 (112)
T ss_pred CCCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHhcCCCcCeeeecccCC
Confidence 3578999998 55999999999 7899999877777643 34455543
No 11
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=79.42 E-value=0.48 Score=35.15 Aligned_cols=29 Identities=31% Similarity=0.602 Sum_probs=22.9
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
-.|..|+.++|-+=+.+..- -..|+|||-
T Consensus 103 VlC~~C~spdT~l~k~~r~~-~l~C~ACGa 131 (138)
T PRK03988 103 VICPECGSPDTKLIKEGRIW-VLKCEACGA 131 (138)
T ss_pred EECCCCCCCCcEEEEcCCeE-EEEcccCCC
Confidence 46999999999997764433 468999995
No 12
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=78.47 E-value=0.57 Score=33.49 Aligned_cols=29 Identities=28% Similarity=0.496 Sum_probs=22.3
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
..|..|+.++|-+=+.+..- -.-|+|||-
T Consensus 81 VlC~~C~spdT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeE-EEEccccCC
Confidence 46999999999998773332 346999983
No 13
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=77.74 E-value=0.59 Score=34.50 Aligned_cols=29 Identities=28% Similarity=0.656 Sum_probs=22.5
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
..|..|+.++|-+-+.+..- -.-|+|||-
T Consensus 98 VlC~~C~sPdT~l~k~~r~~-~l~C~ACGa 126 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVS-LLKCEACGA 126 (133)
T ss_pred EECCCCCCCCcEEEEeCCeE-EEecccCCC
Confidence 46999999999998754332 358999995
No 14
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=74.06 E-value=1.6 Score=36.57 Aligned_cols=32 Identities=34% Similarity=0.742 Sum_probs=28.1
Q ss_pred CCCCcccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 11 NEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 11 ~~~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
......|++|+++. |.|-.-.-| ..||-.|-=
T Consensus 17 ~~~Nk~CaDCga~~-P~W~S~nlG-vfiCi~Cag 48 (319)
T COG5347 17 DSSNKKCADCGAPN-PTWASVNLG-VFLCIDCAG 48 (319)
T ss_pred ccccCccccCCCCC-CceEecccC-eEEEeecch
Confidence 44578899999999 999999999 899999944
No 15
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=73.78 E-value=0.85 Score=35.46 Aligned_cols=29 Identities=28% Similarity=0.515 Sum_probs=22.9
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
-.|..|+.++|-+=+.+..- ..-|+|||-
T Consensus 99 V~C~~C~~pdT~l~k~~~~~-~l~C~aCGa 127 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVL-MLRCDACGA 127 (201)
T ss_pred EECCCCCCCCcEEEEcCCeE-EEEcccCCC
Confidence 46999999999997764332 358999996
No 16
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=71.36 E-value=2.3 Score=39.00 Aligned_cols=38 Identities=24% Similarity=0.566 Sum_probs=29.8
Q ss_pred CCCCcccccCCCCCCCccccCCCC---CCccchHHHHHHHH
Q 033547 11 NEMNKSCIDCHTTRTPLWRGGPAG---PRSLCNACGIRYRK 48 (117)
Q Consensus 11 ~~~~~~C~~C~tt~Tp~WR~gp~G---~~~lCNaCGl~~~k 48 (117)
...+-.|..|.|.-||.|+.-+.+ ++.+|.+|----.|
T Consensus 459 a~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSnqk 499 (706)
T KOG3740|consen 459 ATEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSNQK 499 (706)
T ss_pred cCCchhhhhcccccccccccccccCcchHHHHHhhhhhccc
Confidence 345789999999999999887655 56899999764433
No 17
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=71.35 E-value=2.6 Score=22.51 Aligned_cols=23 Identities=26% Similarity=0.765 Sum_probs=15.4
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
.+.|.+||+...+ + ..+|..||-
T Consensus 2 ~~~Cp~Cg~~~~~-------~-~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEIDP-------D-AKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCCc-------c-cccChhhCC
Confidence 3578899885433 2 468888874
No 18
>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=70.36 E-value=1.5 Score=25.83 Aligned_cols=26 Identities=23% Similarity=0.782 Sum_probs=17.4
Q ss_pred ccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 16 SCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 16 ~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
.|.+|+.+. ..+- ...| ..+|..||+
T Consensus 2 ~Cp~Cg~~~-~~~D-~~~g-~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKE-IVFD-PERG-ELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSE-EEEE-TTTT-EEEETTT-B
T ss_pred CCcCCcCCc-eEEc-CCCC-eEECCCCCC
Confidence 589999977 3332 3345 679999997
No 19
>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=68.35 E-value=1.3 Score=32.30 Aligned_cols=28 Identities=32% Similarity=0.604 Sum_probs=22.9
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHH
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACG 43 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCG 43 (117)
-.|..|+.++|-+=+.+..- ..-|+|||
T Consensus 94 VlC~~C~spdT~l~k~~r~~-~l~C~aCG 121 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLI-FLKCKACG 121 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCC-EEEETTTS
T ss_pred EEcCCCCCCccEEEEcCCEE-EEEecccC
Confidence 46999999999998775544 56899998
No 20
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=68.10 E-value=2.7 Score=38.28 Aligned_cols=45 Identities=24% Similarity=0.451 Sum_probs=31.2
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHHHHHH-hcccccCCCCc
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRK-TKKLALLGRDK 59 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k-~~~~rp~~~~~ 59 (117)
..+.|++|+... |.|-.-..| -.+|-.|.=-.|. ..+.+.+.|++
T Consensus 22 gNk~CADCgs~~-P~WASiNlG-IFICi~CSGIHRsLGhRVKSLSLDk 67 (648)
T PLN03119 22 PNRRCINCNSLG-PQYVCTTFW-TFVCMACSGIHREFTHRVKSVSMSK 67 (648)
T ss_pred CCCccccCCCCC-CCceeeccc-eEEeccchhhhccCCceeeccccCC
Confidence 568899999866 999999999 7899999433332 22344444433
No 21
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=66.13 E-value=4.6 Score=34.91 Aligned_cols=45 Identities=29% Similarity=0.521 Sum_probs=33.5
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHHHHHHhcc----cccCCCCc
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKK----LALLGRDK 59 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~~~----~rp~~~~~ 59 (117)
....|.+|+... |.|-.-..| ..+|..|.=..|..+. .|.+.|+.
T Consensus 21 gNk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRsLGvHISfVRSltLD~ 69 (395)
T PLN03114 21 DNKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRSLGVHISFVRSTNLDS 69 (395)
T ss_pred CCCcCccCCCCC-CCceeeccc-eeehhhhhHhhccCCCCCceeecccCCC
Confidence 567899999865 999999999 7999999655555443 34555553
No 22
>PLN03131 hypothetical protein; Provisional
Probab=63.20 E-value=4.1 Score=37.45 Aligned_cols=45 Identities=20% Similarity=0.399 Sum_probs=30.9
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHHHHHHh-cccccCCCCc
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT-KKLALLGRDK 59 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~-~~~rp~~~~~ 59 (117)
..+.|++|+.. -|.|-.-..| ..+|-.|.=..|.. .+.+.+.|++
T Consensus 22 gNk~CADCga~-~P~WASiNlG-IFICi~CSGIHRsLghRVKSVTLD~ 67 (705)
T PLN03131 22 PNRRCINCNSL-GPQFVCTNFW-TFICMTCSGIHREFTHRVKSVSMSK 67 (705)
T ss_pred CCCccccCCCC-CCCeeEeccc-eEEchhchhhhcccCcccccccCCC
Confidence 56789999975 4999998899 78999994333322 2344444433
No 23
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=62.98 E-value=1.8 Score=27.57 Aligned_cols=23 Identities=26% Similarity=0.800 Sum_probs=17.7
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHHH
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIR 45 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~ 45 (117)
.-.|.+||...-| +.+|..||.|
T Consensus 27 l~~C~~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 27 LVECPNCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred ceECCCCCCccCC---------eEECCCCCcC
Confidence 4569999877655 6799999965
No 24
>PF15396 FAM60A: Protein Family FAM60A
Probab=60.82 E-value=5.7 Score=31.79 Aligned_cols=22 Identities=27% Similarity=0.534 Sum_probs=17.4
Q ss_pred ccchHHHHHHHHhcccccCCCCc
Q 033547 37 SLCNACGIRYRKTKKLALLGRDK 59 (117)
Q Consensus 37 ~lCNaCGl~~~k~~~~rp~~~~~ 59 (117)
.+||||-|..++. +..|.|.++
T Consensus 50 eICNACVLLVKRw-KKLP~Gs~r 71 (213)
T PF15396_consen 50 EICNACVLLVKRW-KKLPPGSKR 71 (213)
T ss_pred hhhHHHHHHHHHH-hhCCCCccc
Confidence 5999999999887 666776644
No 25
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=59.80 E-value=2 Score=28.38 Aligned_cols=34 Identities=21% Similarity=0.334 Sum_probs=25.3
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHHHHH
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYR 47 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~ 47 (117)
.-.|..|.+..|-.|.+-.+-+..-|-+||...+
T Consensus 10 GA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~ 43 (66)
T COG3529 10 GAVCPACQAQDTLAMWRENNVEIVECVKCGHHMR 43 (66)
T ss_pred cCCCcccchhhHHHHHHhcCCceEehhhcchHhh
Confidence 4579999999996654444444789999998653
No 26
>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=59.43 E-value=3.1 Score=24.98 Aligned_cols=25 Identities=44% Similarity=1.070 Sum_probs=18.7
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHH
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACG 43 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCG 43 (117)
...|..| .+|+.| ..+| ..+|-+|+
T Consensus 17 ~~~Cp~C---~~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDC---GTPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred cCccCCC---CCeeEE-ecCC-CEECCCCC
Confidence 3568888 489998 4466 68998885
No 27
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=58.18 E-value=2.4 Score=29.95 Aligned_cols=35 Identities=14% Similarity=0.255 Sum_probs=22.8
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
.-.|.+|+...-+. ..+...++..|..||.|+...
T Consensus 21 ~f~CP~Cge~~v~v-~~~k~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 21 IFECPRCGKVSISV-KIKKNIAIITCGNCGLYTEFE 55 (99)
T ss_pred EeECCCCCCeEeee-ecCCCcceEECCCCCCccCEE
Confidence 45799999532221 112245578999999987664
No 28
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=56.67 E-value=4.2 Score=33.83 Aligned_cols=27 Identities=37% Similarity=0.844 Sum_probs=25.0
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHH
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNAC 42 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaC 42 (117)
.+.|++|++. .|.|-.-..| ..+|-.|
T Consensus 25 N~~CADC~a~-~P~WaSwnlG-vFiC~~C 51 (287)
T KOG0703|consen 25 NKVCADCGAK-GPRWASWNLG-VFICLRC 51 (287)
T ss_pred cCcccccCCC-CCCeEEeecC-eEEEeec
Confidence 6789999999 9999999999 7899998
No 29
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=55.59 E-value=6.2 Score=35.34 Aligned_cols=42 Identities=19% Similarity=0.297 Sum_probs=26.5
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHHHHHHHhcccccCCCCc
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKKLALLGRDK 59 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~~~~rp~~~~~ 59 (117)
.+|.||+.+.--. .++.....|++||.-......-.-+++-.
T Consensus 1 ~~C~~C~~s~fe~---d~a~g~~~C~~CG~v~E~~~ivsev~F~e 42 (521)
T KOG1598|consen 1 MVCKNCGGSNFER---DEATGNLYCTACGTVLEYNNIVAEVTFVE 42 (521)
T ss_pred CcCCCCCCCCccc---ccccCCceeccccceeeccceeEEeeeec
Confidence 4699999876433 44333789999998665554333344433
No 30
>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=54.81 E-value=5.1 Score=23.25 Aligned_cols=27 Identities=30% Similarity=0.707 Sum_probs=20.6
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
....|..|+.. |-...+| ...|..||-
T Consensus 7 ~~~~C~~C~~~----~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 7 PNEPCPVCGSR----WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CCCcCCCCCCe----EeEccCC-EEEhhhCce
Confidence 34569999987 6566778 789999984
No 31
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=53.96 E-value=11 Score=24.31 Aligned_cols=29 Identities=34% Similarity=0.666 Sum_probs=22.3
Q ss_pred CCcccccCCCCCCCccccCCCCCCccc-hHHHHHHHHh
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLC-NACGIRYRKT 49 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lC-NaCGl~~~k~ 49 (117)
+-+.|.+||.+.-|. +.+| ..|+--|.++
T Consensus 2 ~HkHC~~CG~~Ip~~--------~~fCS~~C~~~~~k~ 31 (59)
T PF09889_consen 2 PHKHCPVCGKPIPPD--------ESFCSPKCREEYRKR 31 (59)
T ss_pred CCCcCCcCCCcCCcc--------hhhhCHHHHHHHHHH
Confidence 346799999766542 6799 5999988876
No 32
>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=53.73 E-value=6.9 Score=23.01 Aligned_cols=29 Identities=21% Similarity=0.602 Sum_probs=21.5
Q ss_pred CcccccCCCCCCCccccCC-CCCCccchHHH
Q 033547 14 NKSCIDCHTTRTPLWRGGP-AGPRSLCNACG 43 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp-~G~~~lCNaCG 43 (117)
...|..|+.+..=.|..-. .| ..+|+.||
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G-~~~C~~Cg 32 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRG-TWFCSVCG 32 (37)
T ss_pred ccCCCCCCCccccccccCCCCc-CEEeCCCC
Confidence 3569999998877775533 45 68999996
No 33
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=53.61 E-value=5.7 Score=32.45 Aligned_cols=31 Identities=19% Similarity=0.584 Sum_probs=18.7
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHHHH
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRY 46 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~ 46 (117)
....|.+|+.+ ..... -..| ..+|..||+-.
T Consensus 10 ~~~~Cp~Cg~~-~iv~d-~~~G-e~vC~~CG~Vl 40 (310)
T PRK00423 10 EKLVCPECGSD-KLIYD-YERG-EIVCADCGLVI 40 (310)
T ss_pred cCCcCcCCCCC-CeeEE-CCCC-eEeecccCCcc
Confidence 44568888852 22222 3456 67888888743
No 34
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=53.09 E-value=8 Score=20.27 Aligned_cols=20 Identities=25% Similarity=0.798 Sum_probs=10.5
Q ss_pred cccCCCCCCCccccCCCCCCccchHHHH
Q 033547 17 CIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 17 C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
|.+||..... + ..+|..||-
T Consensus 2 Cp~CG~~~~~-------~-~~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIED-------D-AKFCPNCGT 21 (23)
T ss_pred CcccCCCCCC-------c-CcchhhhCC
Confidence 5666654432 2 346666663
No 35
>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=53.08 E-value=2.3 Score=23.60 Aligned_cols=27 Identities=30% Similarity=0.731 Sum_probs=15.3
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
.+.|..||....+. +.|-...|.+||.
T Consensus 3 ~rfC~~CG~~t~~~----~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA----PGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-----SSSS-EEESSSS-
T ss_pred CcccCcCCccccCC----CCcCEeECCCCcC
Confidence 46799999887765 3455678888886
No 36
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=52.97 E-value=4.4 Score=33.56 Aligned_cols=34 Identities=24% Similarity=0.449 Sum_probs=26.1
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 12 EMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 12 ~~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
...+.|..||+...|. ..|-..+|+.||..+.-.
T Consensus 109 ~~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~fPR 142 (279)
T COG2816 109 RSHRFCGRCGTKTYPR----EGGWARVCPKCGHEHFPR 142 (279)
T ss_pred hhCcCCCCCCCcCccc----cCceeeeCCCCCCccCCC
Confidence 3468899999998886 445568999999876543
No 37
>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=52.49 E-value=3.1 Score=27.70 Aligned_cols=35 Identities=20% Similarity=0.376 Sum_probs=26.7
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHHHHHH
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRK 48 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k 48 (117)
.-.|..|+...|-+|....+-...-|-+||.....
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~ 42 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQ 42 (71)
T ss_pred CccCCCCcCccEEEEEEeCCceEEEecCCCCeecc
Confidence 35799999999988655555557899999985443
No 38
>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=48.34 E-value=8.4 Score=24.22 Aligned_cols=29 Identities=21% Similarity=0.574 Sum_probs=21.1
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHHH
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIR 45 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~ 45 (117)
....|+.||..... ...+....|..||..
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 56789999987665 334445799999873
No 39
>PRK00420 hypothetical protein; Validated
Probab=47.52 E-value=7.5 Score=28.07 Aligned_cols=29 Identities=31% Similarity=0.622 Sum_probs=21.2
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHHHHH
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYR 47 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~ 47 (117)
...|..|| +|+.|- ..| +.+|-.||-.+.
T Consensus 23 ~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCC---Ccceec-CCC-ceECCCCCCeee
Confidence 46798998 677664 556 689999997443
No 40
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=47.12 E-value=32 Score=22.66 Aligned_cols=44 Identities=23% Similarity=0.486 Sum_probs=32.6
Q ss_pred CCCcccccCCCCCCCc--cccC-CCCCCccchHHHHHHHHhcccccC
Q 033547 12 EMNKSCIDCHTTRTPL--WRGG-PAGPRSLCNACGIRYRKTKKLALL 55 (117)
Q Consensus 12 ~~~~~C~~C~tt~Tp~--WR~g-p~G~~~lCNaCGl~~~k~~~~rp~ 55 (117)
.....|..|..+.|-- .-.. ..-|..+|-+|--||-.-+..|-+
T Consensus 3 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnV 49 (63)
T PF02701_consen 3 EQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNV 49 (63)
T ss_pred ccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCC
Confidence 3567899999988754 2332 245678999999999998876644
No 41
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=44.54 E-value=2.3 Score=34.37 Aligned_cols=32 Identities=19% Similarity=0.240 Sum_probs=19.4
Q ss_pred CcccccCCCCCCCc-cccC-CCCCCccchHHHHH
Q 033547 14 NKSCIDCHTTRTPL-WRGG-PAGPRSLCNACGIR 45 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~-WR~g-p~G~~~lCNaCGl~ 45 (117)
...|..|+...... +... ..+.-+.|..||-+
T Consensus 122 ~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 155 (250)
T COG0846 122 RVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGP 155 (250)
T ss_pred eeEeCCCcCccchhhhhhhcccCCCCcCccCCCc
Confidence 46799998765533 2222 22224689999874
No 42
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=44.19 E-value=12 Score=24.39 Aligned_cols=16 Identities=19% Similarity=0.553 Sum_probs=13.9
Q ss_pred cccccCCCCC-CCcccc
Q 033547 15 KSCIDCHTTR-TPLWRG 30 (117)
Q Consensus 15 ~~C~~C~tt~-Tp~WR~ 30 (117)
..|.+|+++. |..|..
T Consensus 16 ~~CP~Cgs~~~T~~W~G 32 (61)
T PRK08351 16 DRCPVCGSRDLSDEWFD 32 (61)
T ss_pred CcCCCCcCCcccccccc
Confidence 3699999998 899986
No 43
>COG3952 Predicted membrane protein [Function unknown]
Probab=43.27 E-value=6.2 Score=28.70 Aligned_cols=20 Identities=30% Similarity=0.413 Sum_probs=14.9
Q ss_pred ccccCCCCCCccchHHHHHHHH
Q 033547 27 LWRGGPAGPRSLCNACGIRYRK 48 (117)
Q Consensus 27 ~WR~gp~G~~~lCNaCGl~~~k 48 (117)
+||.+|-+ .+|++||++-..
T Consensus 76 i~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHhcchHH--HHHHhhhHHHHH
Confidence 36667766 699999987544
No 44
>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=42.86 E-value=10 Score=22.33 Aligned_cols=31 Identities=26% Similarity=0.589 Sum_probs=18.7
Q ss_pred cccccCCCCCCCcc--ccCCCCCCccchHHHHHH
Q 033547 15 KSCIDCHTTRTPLW--RGGPAGPRSLCNACGIRY 46 (117)
Q Consensus 15 ~~C~~C~tt~Tp~W--R~gp~G~~~lCNaCGl~~ 46 (117)
+.|+-||.+.+..= =.||++ ...|+.|-..-
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~-~~IC~~Cv~~~ 34 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNG-AYICDECVEQA 34 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-S-EEEEHHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCC-cEECHHHHHHH
Confidence 57999999887541 256766 68999997643
No 45
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=42.17 E-value=17 Score=23.83 Aligned_cols=34 Identities=29% Similarity=0.448 Sum_probs=24.7
Q ss_pred CCCCcccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 11 NEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 11 ~~~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
+...-.|.+|+...|-. .+...-|-.||.+.-++
T Consensus 17 ~~miYiCgdC~~en~lk-----~~D~irCReCG~RIlyK 50 (62)
T KOG3507|consen 17 ATMIYICGDCGQENTLK-----RGDVIRCRECGYRILYK 50 (62)
T ss_pred ccEEEEecccccccccc-----CCCcEehhhcchHHHHH
Confidence 33466899999988865 34467899999765554
No 46
>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=41.91 E-value=5.8 Score=25.80 Aligned_cols=33 Identities=18% Similarity=0.274 Sum_probs=24.3
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHHHH
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRY 46 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~ 46 (117)
.-.|..|+...|-+|-....-...-|-.||...
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred cccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 357999999999775444444467999999743
No 47
>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=41.25 E-value=6.9 Score=23.01 Aligned_cols=28 Identities=21% Similarity=0.412 Sum_probs=17.6
Q ss_pred ccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 16 SCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 16 ~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
.|.+||..-+-+..-.. .+...|-.||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 58888876555543333 33567888874
No 48
>PF12773 DZR: Double zinc ribbon
Probab=41.25 E-value=16 Score=21.56 Aligned_cols=27 Identities=30% Similarity=0.683 Sum_probs=15.4
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
....|.+||+.-. .+......|..||-
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGA 37 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcC
Confidence 4567777777666 22222346666664
No 49
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=40.89 E-value=8.4 Score=23.25 Aligned_cols=29 Identities=21% Similarity=0.428 Sum_probs=20.5
Q ss_pred ccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 16 SCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 16 ~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
.|.+||...+.. +.+ ..-|..||-+.-.+
T Consensus 4 ~C~~Cg~~~~~~----~~~-~irC~~CG~rIlyK 32 (44)
T smart00659 4 ICGECGRENEIK----SKD-VVRCRECGYRILYK 32 (44)
T ss_pred ECCCCCCEeecC----CCC-ceECCCCCceEEEE
Confidence 699999987765 223 57899999654443
No 50
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=40.77 E-value=15 Score=31.17 Aligned_cols=29 Identities=24% Similarity=0.622 Sum_probs=21.8
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
....|.|||...|+-. ++|..-+|-+||-
T Consensus 314 k~nfc~ncG~~~t~~~---~ng~a~fcp~cgq 342 (345)
T COG4260 314 KLNFCLNCGCGTTADF---DNGKAKFCPECGQ 342 (345)
T ss_pred ccccccccCcccccCC---ccchhhhChhhcC
Confidence 3458999998888863 4554559999984
No 51
>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=40.45 E-value=4.7 Score=25.27 Aligned_cols=21 Identities=29% Similarity=0.865 Sum_probs=15.2
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHH
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACG 43 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCG 43 (117)
...|.+||... -++.+|..||
T Consensus 26 l~~c~~cg~~~---------~~H~vc~~cG 46 (56)
T PF01783_consen 26 LVKCPNCGEPK---------LPHRVCPSCG 46 (56)
T ss_dssp EEESSSSSSEE---------STTSBCTTTB
T ss_pred eeeeccCCCEe---------cccEeeCCCC
Confidence 45688888533 2468999999
No 52
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=39.51 E-value=12 Score=29.63 Aligned_cols=24 Identities=25% Similarity=0.485 Sum_probs=13.8
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
+...|.+||.+.+.- ..+|..||-
T Consensus 353 p~~~c~~cg~~~~~~--------~~~c~~c~~ 376 (389)
T PRK11788 353 PRYRCRNCGFTARTL--------YWHCPSCKA 376 (389)
T ss_pred CCEECCCCCCCCccc--------eeECcCCCC
Confidence 345577777665443 456666654
No 53
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=38.99 E-value=14 Score=32.58 Aligned_cols=37 Identities=32% Similarity=0.683 Sum_probs=29.5
Q ss_pred CCCCcccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 11 NEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 11 ~~~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
....++|.+|+. .-|-|-.-+.| -.||--|---.|--
T Consensus 20 ~~~NKvCFDCgA-knPtWaSVTYG-IFLCiDCSAvHRnL 56 (454)
T KOG0706|consen 20 QSENKVCFDCGA-KNPTWASVTYG-IFLCIDCSAVHRNL 56 (454)
T ss_pred CCCCceecccCC-CCCCceeecce-EEEEEecchhhhcc
Confidence 446789999997 46999999999 89999996644433
No 54
>PF10897 DUF2713: Protein of unknown function (DUF2713); InterPro: IPR020404 This entry contains proteins with no known function. In some organisms this represents the C-terminal domain of a fusion protein with YjbL.
Probab=38.20 E-value=12 Score=30.20 Aligned_cols=15 Identities=60% Similarity=0.884 Sum_probs=13.4
Q ss_pred HHHHHHhhhcccccC
Q 033547 103 AAILLMSLSYGCLYA 117 (117)
Q Consensus 103 AA~lLm~lS~g~~~~ 117 (117)
-|.||.++||||+||
T Consensus 120 lAsll~S~sy~Sa~A 134 (246)
T PF10897_consen 120 LASLLISFSYGSAYA 134 (246)
T ss_pred HHHHHHHHHHhHHHH
Confidence 388999999999986
No 55
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=37.41 E-value=19 Score=28.10 Aligned_cols=9 Identities=56% Similarity=0.822 Sum_probs=6.4
Q ss_pred CHH-HHHHHH
Q 033547 98 GEE-EQAAIL 106 (117)
Q Consensus 98 ~Ee-e~AA~l 106 (117)
.|| |+||++
T Consensus 151 ~EefEeAA~i 160 (176)
T COG3880 151 REEFEEAAVI 160 (176)
T ss_pred HHHHHHHHHH
Confidence 445 899975
No 56
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=36.17 E-value=17 Score=27.95 Aligned_cols=28 Identities=21% Similarity=0.628 Sum_probs=23.4
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHH
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACG 43 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCG 43 (117)
..|..||+.....|-.-+.| ..+|..|+
T Consensus 150 ~~C~~Cg~~~~~~~f~~~~g-g~~c~~c~ 177 (247)
T PRK00085 150 DHCAVCGAPGDHRYFSPKEG-GAVCSECG 177 (247)
T ss_pred hhHhcCCCCCCceEEecccC-Cccccccc
Confidence 47999999887777777777 78999997
No 57
>PF14227 UBN2_2: gag-polypeptide of LTR copia-type
Probab=35.72 E-value=29 Score=23.54 Aligned_cols=26 Identities=31% Similarity=0.436 Sum_probs=20.6
Q ss_pred hhhhhhccCCCCHHHHHHHHHHhhhc
Q 033547 87 KAGLMAVGSDMGEEEQAAILLMSLSY 112 (117)
Q Consensus 87 k~~~~~~g~~~~Eee~AA~lLm~lS~ 112 (117)
-.+|...|..+.|+..+.+||.+|..
T Consensus 52 ~~~L~~~g~~i~d~~~~~~lL~sLP~ 77 (119)
T PF14227_consen 52 VNQLKSLGVPIDDEDKVIILLSSLPP 77 (119)
T ss_pred HHhhccccccchHHHHHHHHHHcCCH
Confidence 34556667789999999999999864
No 58
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=35.42 E-value=23 Score=23.34 Aligned_cols=17 Identities=29% Similarity=0.567 Sum_probs=12.8
Q ss_pred CcccccCCCCC-CCcccc
Q 033547 14 NKSCIDCHTTR-TPLWRG 30 (117)
Q Consensus 14 ~~~C~~C~tt~-Tp~WR~ 30 (117)
...|.+||++. |+.|..
T Consensus 17 ~~~Cp~Cgs~~~S~~w~G 34 (64)
T PRK06393 17 EKTCPVHGDEKTTTEWFG 34 (64)
T ss_pred CCcCCCCCCCcCCcCcce
Confidence 34799999987 677864
No 59
>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=35.31 E-value=12 Score=22.26 Aligned_cols=29 Identities=21% Similarity=0.486 Sum_probs=18.9
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
-.|.+|+..-+ .|+.-.+.+...|-.||-
T Consensus 6 y~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFE-VLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeE-EEEecCCCCCCCCCCCCC
Confidence 36889997555 455433333567999986
No 60
>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=35.30 E-value=11 Score=22.30 Aligned_cols=26 Identities=31% Similarity=0.563 Sum_probs=17.8
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHH
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACG 43 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCG 43 (117)
.+|.+|+.+ ...|-++ .+ ..-|++|+
T Consensus 19 ~~CP~Cg~~-~~~~~~~-~~-~~~C~~C~ 44 (46)
T PF12760_consen 19 FVCPHCGST-KHYRLKT-RG-RYRCKACR 44 (46)
T ss_pred CCCCCCCCe-eeEEeCC-CC-eEECCCCC
Confidence 559999988 5555444 33 57888885
No 61
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=34.73 E-value=16 Score=20.76 Aligned_cols=25 Identities=32% Similarity=0.691 Sum_probs=15.3
Q ss_pred ccccCCCCCCCccccCCCCCCccchHHHHH
Q 033547 16 SCIDCHTTRTPLWRGGPAGPRSLCNACGIR 45 (117)
Q Consensus 16 ~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~ 45 (117)
.|.+|+....-. + ++..-|..||-+
T Consensus 2 ~C~~Cg~~~~~~----~-~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVELK----P-GDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE-BS----T-SSTSSBSSSS-S
T ss_pred CCCcCCCeeEcC----C-CCcEECCcCCCe
Confidence 488999887722 2 224688888853
No 62
>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=34.26 E-value=8.7 Score=24.20 Aligned_cols=23 Identities=26% Similarity=0.749 Sum_probs=16.0
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHHH
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIR 45 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~ 45 (117)
.-.|.+||...- ++.+|-.||.|
T Consensus 26 l~~C~~cG~~~~---------~H~vc~~cG~Y 48 (55)
T TIGR01031 26 LVVCPNCGEFKL---------PHRVCPSCGYY 48 (55)
T ss_pred ceECCCCCCccc---------CeeECCccCeE
Confidence 456888886543 36799999954
No 63
>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=34.05 E-value=15 Score=21.43 Aligned_cols=31 Identities=26% Similarity=0.599 Sum_probs=18.1
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
+.+|..|++---|.=.=...|....||-|+.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCC
Confidence 4679999998777765566665679999986
No 64
>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=33.12 E-value=10 Score=31.39 Aligned_cols=34 Identities=21% Similarity=0.557 Sum_probs=24.2
Q ss_pred CCcccccCCCCCCCcc----ccCCCCCC---ccchHHHHHHH
Q 033547 13 MNKSCIDCHTTRTPLW----RGGPAGPR---SLCNACGIRYR 47 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~W----R~gp~G~~---~lCNaCGl~~~ 47 (117)
....|..|+-.....| |....+ . +.|..||-+|+
T Consensus 257 ~~~~C~~C~~~~~~~~q~QtrsaDEp-mT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQLQTRSADEP-MTTFVTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEecccCCCCC-CeEEEEcCCCCCeee
Confidence 4578999998887766 333322 3 38999998876
No 65
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=32.62 E-value=18 Score=30.47 Aligned_cols=33 Identities=27% Similarity=0.704 Sum_probs=24.4
Q ss_pred ccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 16 SCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 16 ~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
.|..|....-.+--+-.+| .++|-.|||-+..+
T Consensus 2 ~c~~C~~~~~~~V~d~~~g-dtvC~~CGlVl~~r 34 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAG-DTVCSECGLVLEDR 34 (308)
T ss_pred CCCCCCCCCCCeeeeccCC-ceecccCCeeeccc
Confidence 5888887766566666677 68999999866544
No 66
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=32.11 E-value=21 Score=21.05 Aligned_cols=27 Identities=30% Similarity=0.679 Sum_probs=17.6
Q ss_pred ccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 16 SCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 16 ~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
.|.+||..-.+. .+.......|..||-
T Consensus 2 FCp~Cg~~l~~~--~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNMLIPK--EGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCccccc--cCCCCCEEECCcCCC
Confidence 689999865444 111123679999995
No 67
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=32.00 E-value=14 Score=27.92 Aligned_cols=30 Identities=27% Similarity=0.490 Sum_probs=24.0
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
-..|..|+...|++-+.+..- ...|-|||-
T Consensus 105 yv~C~~c~s~dt~l~~~~R~~-~l~c~acGa 134 (151)
T COG1601 105 YVKCKECGSPDTELIKEERLL-FLKCEACGA 134 (151)
T ss_pred eeEeccCCCCchhhhhhhhhH-hhHHHHhCC
Confidence 357999999999998875444 468999995
No 68
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=31.73 E-value=13 Score=23.78 Aligned_cols=23 Identities=9% Similarity=-0.078 Sum_probs=15.1
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHHHH
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRY 46 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~ 46 (117)
...|.+||+..-| +.+|. ||.|.
T Consensus 27 ~~~c~~cg~~~~p---------H~vc~-cG~Y~ 49 (60)
T PRK01110 27 LSVDKTTGEYHLP---------HHVSP-KGYYK 49 (60)
T ss_pred eeEcCCCCceecc---------ceecC-CcccC
Confidence 3467888765544 46788 88654
No 69
>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=31.48 E-value=41 Score=22.85 Aligned_cols=33 Identities=30% Similarity=0.516 Sum_probs=23.9
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 12 EMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 12 ~~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
.....|.-|+...+-. -.| ...|+||..+|++.
T Consensus 4 ~~~~~C~VCg~~~~g~----hyG-v~sC~aCk~FFRR~ 36 (90)
T cd07168 4 ESPKLCSICEDKATGL----HYG-IITCEGCKGFFKRT 36 (90)
T ss_pred ccCCCCcccCCcCcce----EEC-ceehhhhhHhhhhh
Confidence 3556799999755432 234 57899999999886
No 70
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=30.92 E-value=17 Score=29.97 Aligned_cols=9 Identities=33% Similarity=1.191 Sum_probs=5.0
Q ss_pred CccchHHHH
Q 033547 36 RSLCNACGI 44 (117)
Q Consensus 36 ~~lCNaCGl 44 (117)
..+|-.||+
T Consensus 20 e~VC~~CG~ 28 (285)
T COG1405 20 EIVCADCGL 28 (285)
T ss_pred eEEeccCCE
Confidence 455666654
No 71
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.73 E-value=15 Score=27.22 Aligned_cols=34 Identities=32% Similarity=0.703 Sum_probs=22.6
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
....|.+||--. +.| |--.+.+.|.+||+-|-.+
T Consensus 20 l~grCP~CGeGr--LF~-gFLK~~p~C~aCG~dyg~~ 53 (126)
T COG5349 20 LRGRCPRCGEGR--LFR-GFLKVVPACEACGLDYGFA 53 (126)
T ss_pred hcCCCCCCCCch--hhh-hhcccCchhhhccccccCC
Confidence 456788888533 222 3333467999999988776
No 72
>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=30.61 E-value=17 Score=21.63 Aligned_cols=27 Identities=19% Similarity=0.458 Sum_probs=15.6
Q ss_pred cccccCCCCCCCc-cccCC-CCCCccchHH
Q 033547 15 KSCIDCHTTRTPL-WRGGP-AGPRSLCNAC 42 (117)
Q Consensus 15 ~~C~~C~tt~Tp~-WR~gp-~G~~~lCNaC 42 (117)
..|..|+.+.-=. |.... .| ..+|+.|
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G-~~~C~~C 32 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRG-TWICRQC 32 (40)
T ss_dssp E--TTTT-TTTEEEETT----S--EEETTT
T ss_pred CCCCCCcCccccccCcCcccCC-CEECCCC
Confidence 3688999877766 76533 35 7899999
No 73
>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=30.52 E-value=42 Score=22.21 Aligned_cols=30 Identities=20% Similarity=0.602 Sum_probs=21.6
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
..|.-|+...+-. -.| ...|+||..++++.
T Consensus 3 ~~C~VCg~~a~g~----hyG-v~sC~aC~~FFRR~ 32 (78)
T cd07172 3 KICLVCSDEASGC----HYG-VLTCGSCKVFFKRA 32 (78)
T ss_pred CCCeecCCcCcce----EEC-ceeehhhHHhHHHH
Confidence 4588888654433 234 56899999999987
No 74
>PF14122 YokU: YokU-like protein
Probab=30.18 E-value=16 Score=25.47 Aligned_cols=33 Identities=30% Similarity=0.808 Sum_probs=21.8
Q ss_pred ccccCCCCC------CCccccCC---------CCCCccchHHHHHHHHh
Q 033547 16 SCIDCHTTR------TPLWRGGP---------AGPRSLCNACGIRYRKT 49 (117)
Q Consensus 16 ~C~~C~tt~------Tp~WR~gp---------~G~~~lCNaCGl~~~k~ 49 (117)
.|.+|+..+ |-.| .-| ..|...|+.||+-|...
T Consensus 1 ~C~wC~~~~a~~~~~tvyW-eLpdGtraIeI~~tP~i~C~~CgmvYq~d 48 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYW-ELPDGTRAIEITDTPAIICSNCGMVYQDD 48 (87)
T ss_pred CcccccCcccccccceEEE-EcCCCceEEEecCCceeeecCCCcEEehh
Confidence 388898853 3335 223 34567999999977654
No 75
>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=29.80 E-value=21 Score=19.20 Aligned_cols=23 Identities=26% Similarity=0.654 Sum_probs=12.6
Q ss_pred cccCCCCCCCccccCCCCCCccchHHH
Q 033547 17 CIDCHTTRTPLWRGGPAGPRSLCNACG 43 (117)
Q Consensus 17 C~~C~tt~Tp~WR~gp~G~~~lCNaCG 43 (117)
|..|+....|. +. +....|-.||
T Consensus 1 C~sC~~~i~~r---~~-~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPR---EQ-AVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCc---cc-CceEeCCCCC
Confidence 55666665554 21 2246677666
No 76
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=29.48 E-value=20 Score=27.64 Aligned_cols=28 Identities=32% Similarity=0.769 Sum_probs=22.1
Q ss_pred ccccCCCCCCCccccCCCC--CCccchHHH
Q 033547 16 SCIDCHTTRTPLWRGGPAG--PRSLCNACG 43 (117)
Q Consensus 16 ~C~~C~tt~Tp~WR~gp~G--~~~lCNaCG 43 (117)
.|.+||.....+++.-..| .-+.|..||
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~ 31 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCG 31 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccC
Confidence 6999999998899875544 236899996
No 77
>PHA00626 hypothetical protein
Probab=28.75 E-value=13 Score=24.16 Aligned_cols=33 Identities=24% Similarity=0.440 Sum_probs=21.6
Q ss_pred ccccCCCCCCCc--cccCCCCCCccchHHHHHHHHh
Q 033547 16 SCIDCHTTRTPL--WRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 16 ~C~~C~tt~Tp~--WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
.|.+|+..+-.. -=+++.. .+.|..||..+.+.
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~sn-rYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSD-DYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCceeeeeceecccCc-ceEcCCCCCeechh
Confidence 588999853221 0124455 68999999988764
No 78
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=28.70 E-value=15 Score=20.52 Aligned_cols=29 Identities=31% Similarity=0.551 Sum_probs=17.7
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
-.|.+|+..-+.. .....+....|..||-
T Consensus 6 y~C~~Cg~~fe~~-~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVL-QKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEE-EecCCCCCCCCCCCCC
Confidence 3688888855432 3222244567888886
No 79
>PF09610 Myco_arth_vir_N: Mycoplasma virulence signal region (Myco_arth_vir_N); InterPro: IPR011732 This entry represents the N-terminal region of a family of large, virulence-associated proteins in Mycoplasma arthritidis and smaller proteins in Mycoplasma capricolum. It includes a probable signal sequence or signal anchor, which, in most instances, has four consecutive Lys residues before the hydrophobic stretch.
Probab=28.59 E-value=30 Score=20.10 Aligned_cols=14 Identities=43% Similarity=0.489 Sum_probs=11.7
Q ss_pred HHHHHHHhhhcccc
Q 033547 102 QAAILLMSLSYGCL 115 (117)
Q Consensus 102 ~AA~lLm~lS~g~~ 115 (117)
-+|.|+-++|.|+|
T Consensus 16 ~~a~l~as~s~g~v 29 (33)
T PF09610_consen 16 LTASLLASGSFGSV 29 (33)
T ss_pred HHHHHHHceeeeeE
Confidence 57888999999885
No 80
>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=28.31 E-value=54 Score=22.32 Aligned_cols=32 Identities=22% Similarity=0.548 Sum_probs=23.8
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
....|.-|+...+-.+ .| ...|+||..+|++.
T Consensus 5 ~~~~C~VCg~~a~g~h----yG-v~sC~aCk~FFRR~ 36 (90)
T cd07169 5 EQRTCLICGDRATGLH----YG-IISCEGCKGFFKRS 36 (90)
T ss_pred cCCCCeecCCcCcceE----EC-cceehhhHHHHHHH
Confidence 4566999997655442 44 57899999999886
No 81
>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=27.97 E-value=53 Score=22.01 Aligned_cols=31 Identities=19% Similarity=0.618 Sum_probs=22.6
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
...|.-|+...+-. -.| ...|+||..+|++.
T Consensus 3 ~~~C~VCg~~a~g~----hyG-v~sC~aCk~FFRR~ 33 (82)
T cd07173 3 QKTCLICGDEASGC----HYG-ALTCGSCKVFFKRA 33 (82)
T ss_pred CCCCeecCCcCcce----EEC-cchhhhHHHHHHHH
Confidence 34599998755433 244 56899999999987
No 82
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=27.96 E-value=53 Score=27.13 Aligned_cols=32 Identities=28% Similarity=0.377 Sum_probs=22.0
Q ss_pred CcccccCCCCCCCc-cccCCCCCCccchHHHHHHHH
Q 033547 14 NKSCIDCHTTRTPL-WRGGPAGPRSLCNACGIRYRK 48 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~-WR~gp~G~~~lCNaCGl~~~k 48 (117)
++.|..|.-+.|-- =.=..+| +||+|--+..+
T Consensus 1 ~~~C~~C~~~~t~p~i~fd~~G---vC~~C~~~~~~ 33 (343)
T TIGR03573 1 MKFCKRCVMPTTRPGITFDEDG---VCSACRNFEEK 33 (343)
T ss_pred CCcCCCCCCCCCCCCeeECCCC---CchhhhhHHhh
Confidence 36799999987643 1123344 99999987754
No 83
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.48 E-value=22 Score=27.26 Aligned_cols=33 Identities=30% Similarity=0.577 Sum_probs=22.0
Q ss_pred CcccccCCCCCCCcccc-------CCCCCCccchHHHHHH
Q 033547 14 NKSCIDCHTTRTPLWRG-------GPAGPRSLCNACGIRY 46 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~-------gp~G~~~lCNaCGl~~ 46 (117)
...|.+|++..--.|-- ++..+-..|+.||-.|
T Consensus 39 I~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 39 ITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCC
Confidence 45788888876655533 3333446999999654
No 84
>PF12553 DUF3742: Protein of unknown function (DUF3742); InterPro: IPR022213 This domain family is found in bacteria, and is approximately 50 amino acids in length. There is a single completely conserved residue Y that may be functionally important.
Probab=27.35 E-value=22 Score=22.46 Aligned_cols=9 Identities=78% Similarity=1.704 Sum_probs=8.3
Q ss_pred CccccCCCC
Q 033547 26 PLWRGGPAG 34 (117)
Q Consensus 26 p~WR~gp~G 34 (117)
|.||.||.|
T Consensus 34 ~E~R~G~~G 42 (54)
T PF12553_consen 34 PEWREGPAG 42 (54)
T ss_pred HhheecCCC
Confidence 889999997
No 85
>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=27.30 E-value=50 Score=22.90 Aligned_cols=31 Identities=23% Similarity=0.604 Sum_probs=22.3
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
...|.-|+...+-. -.| ...|+||..+|++.
T Consensus 4 ~~~C~VCg~~a~g~----hyG-v~sC~aCk~FFRR~ 34 (97)
T cd07170 4 KRLCLVCGDIASGY----HYG-VASCEACKAFFKRT 34 (97)
T ss_pred CCCCeecCCcCcce----EEC-ceeehhhhHHHHHH
Confidence 45699998654422 245 57899999999886
No 86
>PF09947 DUF2180: Uncharacterized protein conserved in archaea (DUF2180); InterPro: IPR017211 This group represents a predicted zinc finger protein, AF1427 type.
Probab=27.20 E-value=36 Score=22.64 Aligned_cols=32 Identities=38% Similarity=0.857 Sum_probs=22.3
Q ss_pred CCcccccCCC---------CCCCccccCCCC---------CCccchHHHH
Q 033547 13 MNKSCIDCHT---------TRTPLWRGGPAG---------PRSLCNACGI 44 (117)
Q Consensus 13 ~~~~C~~C~t---------t~Tp~WR~gp~G---------~~~lCNaCGl 44 (117)
...+|.-||. .++|+|..+... |+.||..|--
T Consensus 15 AVavCivCG~GlC~~H~~~e~~~~~~g~yp~~~~~~~~~l~RilC~~C~~ 64 (68)
T PF09947_consen 15 AVAVCIVCGAGLCMDHSKREEIPVWEGGYPFPSKKLKKPLPRILCPECHA 64 (68)
T ss_pred ceehHHhcCchhhHHHHhhhheeeeccCCCCccccccCCCCeeecHHHHH
Confidence 4567888886 367889655433 4579999864
No 87
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=27.14 E-value=14 Score=22.65 Aligned_cols=29 Identities=31% Similarity=0.698 Sum_probs=21.8
Q ss_pred CcccccCCCCCCCcc----ccCCCCCCccchHHHH
Q 033547 14 NKSCIDCHTTRTPLW----RGGPAGPRSLCNACGI 44 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~W----R~gp~G~~~lCNaCGl 44 (117)
...|..|+..-+|.. +++ +. -..|..||-
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~-~~-i~~Cp~CgR 54 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKG-DE-IVFCPNCGR 54 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcC-CC-eEECcCCCc
Confidence 458999999999884 455 33 478999983
No 88
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.49 E-value=33 Score=26.40 Aligned_cols=24 Identities=29% Similarity=0.625 Sum_probs=18.0
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHHH
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIR 45 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~ 45 (117)
....|+.||. ..+....|..||..
T Consensus 308 tS~~C~~cg~---------~~~r~~~C~~cg~~ 331 (364)
T COG0675 308 TSKTCPCCGH---------LSGRLFKCPRCGFV 331 (364)
T ss_pred CcccccccCC---------ccceeEECCCCCCe
Confidence 4567999999 33446799999964
No 89
>PF09698 GSu_C4xC__C2xCH: Geobacter CxxxxCH...CXXCH motif (GSu_C4xC__C2xCH); InterPro: IPR010176 This motif occurs from three to eight times in eight different proteins of Geobacter sulfurreducens. The final CXXCH motif matches the cytochrome c family haem-binding site signature, suggesting that the sequence may be involved in haem-binding.
Probab=24.24 E-value=41 Score=19.21 Aligned_cols=18 Identities=33% Similarity=0.981 Sum_probs=13.4
Q ss_pred CCCCCccccCCCCCCccchHH
Q 033547 22 TTRTPLWRGGPAGPRSLCNAC 42 (117)
Q Consensus 22 tt~Tp~WR~gp~G~~~lCNaC 42 (117)
...||.|-.+.... |+.|
T Consensus 18 ~~~~p~W~~~~~~~---C~~C 35 (36)
T PF09698_consen 18 SYTTPTWGSGATTA---CGSC 35 (36)
T ss_pred cccCceeCCCCCCc---cccc
Confidence 34678998888772 8887
No 90
>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=23.91 E-value=66 Score=22.14 Aligned_cols=31 Identities=19% Similarity=0.458 Sum_probs=23.0
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
...|.-|+...+-.+ .| ...|++|..+|++.
T Consensus 5 ~~~C~VCg~~~~g~h----yG-v~sC~aC~~FFRR~ 35 (95)
T cd06968 5 VIPCKICGDKSSGIH----YG-VITCEGCKGFFRRS 35 (95)
T ss_pred ccCCcccCCcCcceE----EC-ceeehhhHHhhHHh
Confidence 346999997655442 44 46899999999987
No 91
>PHA02998 RNA polymerase subunit; Provisional
Probab=23.85 E-value=21 Score=28.23 Aligned_cols=36 Identities=25% Similarity=0.652 Sum_probs=26.2
Q ss_pred CCcccccCCCCCCCcc----ccCCCCC--CccchHHHHHHHH
Q 033547 13 MNKSCIDCHTTRTPLW----RGGPAGP--RSLCNACGIRYRK 48 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~W----R~gp~G~--~~lCNaCGl~~~k 48 (117)
....|..|+-..+--| |.+..++ -..|..||-.|+-
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 4578999999988777 6666552 1389999985543
No 92
>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=23.83 E-value=70 Score=21.38 Aligned_cols=30 Identities=17% Similarity=0.462 Sum_probs=21.8
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
..|.-|+...+-. -.| ...|+||..++++.
T Consensus 4 ~~C~VCg~~~~g~----hyG-v~sC~aC~~FFRR~ 33 (82)
T cd07171 4 HFCAVCSDYASGY----HYG-VWSCEGCKAFFKRS 33 (82)
T ss_pred CCCeecCCcCcce----EEC-ceeehhhHHhHHHH
Confidence 4588898755433 234 56899999999987
No 93
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=23.59 E-value=57 Score=19.18 Aligned_cols=29 Identities=21% Similarity=0.527 Sum_probs=19.6
Q ss_pred ccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 16 SCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 16 ~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
.|..|....++.|+=..-..-.||..|-.
T Consensus 2 ~C~~C~~~~~~r~~C~~C~dfDLC~~C~~ 30 (41)
T cd02337 2 TCNECKHHVETRWHCTVCEDYDLCITCYN 30 (41)
T ss_pred cCCCCCCcCCCceECCCCcchhhHHHHhC
Confidence 47777776678887655443468888854
No 94
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=22.76 E-value=30 Score=27.66 Aligned_cols=32 Identities=25% Similarity=0.430 Sum_probs=22.6
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchHHHHHHHH
Q 033547 13 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRK 48 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k 48 (117)
..+.|..||+..... ..+....|.+||..+.-
T Consensus 98 ~~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 98 SHRFCGYCGHPMHPS----KTEWAMLCPHCRERYYP 129 (256)
T ss_pred cCccccccCCCCeec----CCceeEECCCCCCEECC
Confidence 467899999975542 34546789999965543
No 95
>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=21.93 E-value=35 Score=21.37 Aligned_cols=36 Identities=17% Similarity=0.257 Sum_probs=24.3
Q ss_pred CCCCCCcccccCCCCCCCccccCCCCCCccchHHHH
Q 033547 9 TFNEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 44 (117)
Q Consensus 9 ~~~~~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl 44 (117)
..+.....|.+|....--.=+.....-++.|-.||-
T Consensus 17 ~~~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 17 PSNRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred ccCceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 356678899999987543334444444678888874
No 96
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=21.88 E-value=25 Score=20.74 Aligned_cols=29 Identities=24% Similarity=0.429 Sum_probs=18.4
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHHHHHH
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYR 47 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~ 47 (117)
-.|.+||+..+.. +......|..||-.+.
T Consensus 4 y~C~~CG~~~~~~----~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELD----EYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEEC----CCCCceECCCCCCeEE
Confidence 4699999876543 2211468999986443
No 97
>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=21.85 E-value=70 Score=20.60 Aligned_cols=28 Identities=25% Similarity=0.567 Sum_probs=18.9
Q ss_pred cccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 17 CIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 17 C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
|.-|+...+-. -.| ...|++|..++++.
T Consensus 1 C~VCg~~~~g~----hyG-v~~C~aC~~FFRR~ 28 (73)
T cd07158 1 CKVCGDKASGF----HYG-VHSCEGCKGFFRRT 28 (73)
T ss_pred CcccCccCcce----EEC-cchhhHHHHHHhhh
Confidence 55566544432 234 56899999999886
No 98
>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=21.73 E-value=23 Score=19.91 Aligned_cols=23 Identities=30% Similarity=0.661 Sum_probs=11.1
Q ss_pred ccccCCCCCCCccccCCCCCCccchHHH
Q 033547 16 SCIDCHTTRTPLWRGGPAGPRSLCNACG 43 (117)
Q Consensus 16 ~C~~C~tt~Tp~WR~gp~G~~~lCNaCG 43 (117)
.|..|+...|= .+|...+|..||
T Consensus 4 ~Cp~C~se~~y-----~D~~~~vCp~C~ 26 (30)
T PF08274_consen 4 KCPLCGSEYTY-----EDGELLVCPECG 26 (30)
T ss_dssp --TTT-----E-----E-SSSEEETTTT
T ss_pred CCCCCCCccee-----ccCCEEeCCccc
Confidence 57888887775 455567888886
No 99
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=21.43 E-value=13 Score=21.77 Aligned_cols=31 Identities=23% Similarity=0.654 Sum_probs=19.1
Q ss_pred ccccCCCCCCCcc----ccCCCCC--CccchHHHHHH
Q 033547 16 SCIDCHTTRTPLW----RGGPAGP--RSLCNACGIRY 46 (117)
Q Consensus 16 ~C~~C~tt~Tp~W----R~gp~G~--~~lCNaCGl~~ 46 (117)
.|.+|+-.+.--| |++.++. -+.|-.||-.|
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 5888887665555 4444441 24788888544
No 100
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=21.30 E-value=81 Score=27.04 Aligned_cols=29 Identities=21% Similarity=0.492 Sum_probs=20.7
Q ss_pred CCcccccCCCCCCCc--cccCCCCCCccchHHH
Q 033547 13 MNKSCIDCHTTRTPL--WRGGPAGPRSLCNACG 43 (117)
Q Consensus 13 ~~~~C~~C~tt~Tp~--WR~gp~G~~~lCNaCG 43 (117)
....|+-||.+.... --.||. ...|+.|-
T Consensus 8 ~~~~CSFCGr~~~ev~~li~g~~--~~IC~~Ci 38 (412)
T PRK05342 8 KLLYCSFCGKSQHEVRKLIAGPG--VYICDECI 38 (412)
T ss_pred CccccCCCCCChhhccccccCCC--CcccchHH
Confidence 455899999987654 234553 47999994
No 101
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.70 E-value=25 Score=21.64 Aligned_cols=29 Identities=28% Similarity=0.458 Sum_probs=20.2
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchHHHHH
Q 033547 12 EMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIR 45 (117)
Q Consensus 12 ~~~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~ 45 (117)
...+.|..|+.. -++... ....|..||.-
T Consensus 18 ~~~~fCP~Cg~~--~m~~~~---~r~~C~~Cgyt 46 (50)
T PRK00432 18 RKNKFCPRCGSG--FMAEHL---DRWHCGKCGYT 46 (50)
T ss_pred EccCcCcCCCcc--hheccC---CcEECCCcCCE
Confidence 356789999975 554333 36799999864
No 102
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=20.49 E-value=88 Score=21.85 Aligned_cols=31 Identities=19% Similarity=0.461 Sum_probs=22.7
Q ss_pred CcccccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 14 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 14 ~~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
...|.-|+...+-. -.| ...|++|..+|++.
T Consensus 18 ~~~C~VCg~~a~g~----hyG-v~sC~aCk~FFRR~ 48 (101)
T cd07160 18 NEVCSVCGDKASGF----HYN-VLSCEGCKGFFRRS 48 (101)
T ss_pred CCCCeecCCcCcce----EEC-cceehhhhhhhhhc
Confidence 45699999755432 234 57899999999886
No 103
>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=20.45 E-value=87 Score=20.33 Aligned_cols=28 Identities=25% Similarity=0.558 Sum_probs=18.7
Q ss_pred cccCCCCCCCccccCCCCCCccchHHHHHHHHh
Q 033547 17 CIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 49 (117)
Q Consensus 17 C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~~k~ 49 (117)
|.-|+...+-. -.| ...|+||..++++.
T Consensus 1 C~VCg~~~~g~----hyg-v~sC~aC~~FFRR~ 28 (74)
T cd07179 1 CRVCGGKSSGF----HFG-ALTCEGCKGFFRRT 28 (74)
T ss_pred CcccCccCcce----EEC-ceeehhHHHHHHHH
Confidence 45566544332 134 46899999999987
No 104
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=20.02 E-value=50 Score=19.09 Aligned_cols=30 Identities=27% Similarity=0.751 Sum_probs=18.4
Q ss_pred CCCcccccCCCCCCCccccCC--CC-CCccchHH
Q 033547 12 EMNKSCIDCHTTRTPLWRGGP--AG-PRSLCNAC 42 (117)
Q Consensus 12 ~~~~~C~~C~tt~Tp~WR~gp--~G-~~~lCNaC 42 (117)
.+...|..|+.++. .-|.|. .| +.++|-.|
T Consensus 3 ~i~v~CP~C~s~~~-v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 3 KIDVHCPRCQSTEG-VKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred cEeeeCCCCCCCCc-ceeCCCCCCCCEeEecCcC
Confidence 35667888987662 334443 44 44677766
No 105
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=20.01 E-value=39 Score=29.30 Aligned_cols=32 Identities=28% Similarity=0.478 Sum_probs=25.0
Q ss_pred cccccCCCCCCCccccCCCCCCccchHHHHHH
Q 033547 15 KSCIDCHTTRTPLWRGGPAGPRSLCNACGIRY 46 (117)
Q Consensus 15 ~~C~~C~tt~Tp~WR~gp~G~~~lCNaCGl~~ 46 (117)
..|..|+-++|-+-=+...+-..-|-|||.+-
T Consensus 97 VlC~~C~NPETel~itk~q~i~~~CkACG~r~ 128 (400)
T KOG2767|consen 97 VLCPSCENPETELIITKKQTISLKCKACGFRS 128 (400)
T ss_pred eeCcCCCCCceeEEecccchhhhHHHHcCCcc
Confidence 36999999999887665555567899999654
Done!