Query 033001
Match_columns 129
No_of_seqs 185 out of 805
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 08:34:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033001.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033001hhsearch_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 99.8 4.8E-19 1E-23 114.4 3.1 50 28-77 1-51 (54)
2 smart00401 ZnF_GATA zinc finge 99.7 8.7E-18 1.9E-22 107.5 3.0 48 25-72 2-50 (52)
3 PF00320 GATA: GATA zinc finge 99.6 7.9E-17 1.7E-21 96.1 1.2 35 29-63 1-35 (36)
4 KOG1601 GATA-4/5/6 transcripti 99.1 8.4E-11 1.8E-15 89.0 2.7 53 26-78 199-251 (340)
5 COG5641 GAT1 GATA Zn-finger-co 99.0 2.5E-10 5.4E-15 100.9 2.3 62 17-79 149-216 (498)
6 KOG3554 Histone deacetylase co 93.9 0.057 1.2E-06 48.8 3.5 40 24-63 384-425 (693)
7 COG5641 GAT1 GATA Zn-finger-co 93.3 0.037 8.1E-07 49.6 1.2 53 26-78 297-350 (498)
8 PF14803 Nudix_N_2: Nudix N-te 82.5 0.25 5.3E-06 29.1 -0.9 29 27-55 1-29 (34)
9 PF01412 ArfGap: Putative GTPa 80.2 1.6 3.5E-05 31.3 2.5 37 24-62 11-47 (116)
10 smart00105 ArfGap Putative GTP 80.0 1.8 4E-05 30.9 2.7 45 25-71 2-50 (112)
11 PRK03988 translation initiatio 78.4 0.53 1.1E-05 35.6 -0.5 30 26-56 102-131 (138)
12 TIGR00311 aIF-2beta translatio 77.2 0.62 1.3E-05 35.0 -0.5 29 27-56 98-126 (133)
13 smart00653 eIF2B_5 domain pres 76.4 0.68 1.5E-05 33.7 -0.4 29 27-56 81-109 (110)
14 COG5347 GTPase-activating prot 73.3 1.7 3.7E-05 37.1 1.1 47 23-71 17-67 (319)
15 PRK12336 translation initiatio 72.0 0.97 2.1E-05 35.8 -0.6 29 27-56 99-127 (201)
16 KOG3740 Uncharacterized conser 71.2 2.6 5.6E-05 39.3 1.9 42 16-57 452-496 (706)
17 PLN03114 ADP-ribosylation fact 68.4 3.6 7.9E-05 36.1 2.1 46 24-71 20-69 (395)
18 PF02701 zf-Dof: Dof domain, z 68.2 9.6 0.00021 25.6 3.6 45 24-68 3-50 (63)
19 PF06677 Auto_anti-p27: Sjogre 67.5 1.8 3.9E-05 26.5 0.0 25 26-55 17-41 (41)
20 PF01873 eIF-5_eIF-2B: Domain 65.7 1.4 3.1E-05 32.6 -0.7 29 27-56 94-122 (125)
21 PF08271 TF_Zn_Ribbon: TFIIB z 65.7 1.8 3.8E-05 25.9 -0.2 26 28-56 2-27 (43)
22 PLN03119 putative ADP-ribosyla 62.7 3.8 8.3E-05 38.0 1.2 46 24-71 21-67 (648)
23 COG3529 Predicted nucleic-acid 61.5 1.4 3.1E-05 29.6 -1.3 33 26-58 10-42 (66)
24 PF13248 zf-ribbon_3: zinc-rib 60.0 5.9 0.00013 21.4 1.2 23 26-56 2-24 (26)
25 KOG3507 DNA-directed RNA polym 59.3 6.2 0.00013 26.3 1.4 38 21-63 15-52 (62)
26 PRK12286 rpmF 50S ribosomal pr 58.7 2.5 5.3E-05 27.5 -0.5 25 24-57 25-49 (57)
27 PLN03131 hypothetical protein; 57.4 5.7 0.00012 37.2 1.4 46 24-71 21-67 (705)
28 PRK14892 putative transcriptio 54.8 3 6.5E-05 30.0 -0.7 36 25-61 20-55 (99)
29 PRK00420 hypothetical protein; 54.1 5.3 0.00012 29.4 0.5 30 25-59 22-51 (112)
30 PF07282 OrfB_Zn_ribbon: Putat 53.4 6.3 0.00014 25.3 0.7 31 23-57 25-55 (69)
31 PF09526 DUF2387: Probable met 53.3 2.8 6.1E-05 28.4 -1.0 34 26-59 8-41 (71)
32 KOG1598 Transcription initiati 52.6 7.5 0.00016 35.4 1.3 31 27-60 1-31 (521)
33 PF09889 DUF2116: Uncharacteri 52.2 13 0.00028 24.4 2.1 31 25-63 2-33 (59)
34 PF15396 FAM60A: Protein Famil 51.0 9.7 0.00021 31.0 1.6 22 49-71 50-71 (213)
35 PF11781 RRN7: RNA polymerase 50.5 7.2 0.00016 23.0 0.6 27 25-56 7-33 (36)
36 smart00778 Prim_Zn_Ribbon Zinc 49.5 8.9 0.00019 22.9 0.9 29 26-55 3-32 (37)
37 COG3952 Predicted membrane pro 49.0 4.2 9.1E-05 30.1 -0.7 20 39-60 76-95 (113)
38 KOG0703 Predicted GTPase-activ 48.9 7.1 0.00015 33.1 0.6 28 26-55 25-52 (287)
39 PRK00423 tfb transcription ini 47.5 7.9 0.00017 32.2 0.6 28 26-56 11-38 (310)
40 COG2816 NPY1 NTP pyrophosphohy 47.3 6.1 0.00013 33.3 -0.1 35 23-61 108-142 (279)
41 PF12773 DZR: Double zinc ribb 44.8 13 0.00028 22.3 1.2 29 23-56 9-37 (50)
42 COG4260 Membrane protease subu 44.5 18 0.00038 31.3 2.3 30 24-56 313-342 (345)
43 TIGR02443 conserved hypothetic 42.8 5.3 0.00012 26.4 -0.9 33 26-58 9-41 (59)
44 PF13240 zinc_ribbon_2: zinc-r 41.6 16 0.00034 19.5 1.0 7 49-55 14-20 (23)
45 PF09723 Zn-ribbon_8: Zinc rib 39.2 8.3 0.00018 23.1 -0.4 28 28-56 7-34 (42)
46 KOG0706 Predicted GTPase-activ 38.0 14 0.00031 33.1 0.8 39 23-63 20-58 (454)
47 smart00659 RPOLCX RNA polymera 37.9 10 0.00022 23.3 -0.1 28 28-60 4-31 (44)
48 PF09297 zf-NADH-PPase: NADH p 37.3 4.8 0.0001 22.7 -1.5 27 26-56 3-29 (32)
49 PRK08351 DNA-directed RNA poly 35.4 20 0.00044 23.7 1.0 16 27-42 16-32 (61)
50 PF04161 Arv1: Arv1-like famil 35.3 14 0.0003 29.1 0.3 28 28-55 2-31 (208)
51 PF12760 Zn_Tnp_IS1595: Transp 35.0 12 0.00025 22.7 -0.2 26 27-55 19-44 (46)
52 PF06689 zf-C4_ClpX: ClpX C4-t 34.9 13 0.00028 22.3 0.0 31 27-58 2-34 (41)
53 PRK00085 recO DNA repair prote 34.6 18 0.00039 28.3 0.8 29 26-55 149-177 (247)
54 KOG4215 Hepatocyte nuclear fac 34.6 1E+02 0.0023 27.5 5.5 37 19-60 12-48 (432)
55 PF14122 YokU: YokU-like prote 33.9 7.7 0.00017 27.6 -1.3 34 28-62 1-49 (87)
56 TIGR02605 CxxC_CxxC_SSSS putat 33.3 15 0.00032 22.3 0.1 28 28-56 7-34 (52)
57 COG1601 GCD7 Translation initi 33.3 13 0.00028 28.6 -0.2 31 25-56 104-134 (151)
58 PF01783 Ribosomal_L32p: Ribos 33.3 7.3 0.00016 24.9 -1.4 22 25-55 25-46 (56)
59 COG0675 Transposase and inacti 33.1 19 0.00041 28.3 0.7 27 22-57 305-331 (364)
60 TIGR01385 TFSII transcription 33.0 11 0.00023 31.9 -0.8 36 23-59 255-297 (299)
61 COG3880 Modulator of heat shoc 32.9 21 0.00045 28.4 0.9 24 95-118 131-160 (176)
62 smart00661 RPOL9 RNA polymeras 32.1 20 0.00044 21.5 0.6 27 27-56 1-28 (52)
63 PF09610 Myco_arth_vir_N: Myco 31.9 22 0.00048 21.0 0.7 15 113-127 15-29 (33)
64 PF10897 DUF2713: Protein of u 31.5 19 0.00042 29.6 0.5 15 115-129 120-134 (246)
65 TIGR03573 WbuX N-acetyl sugar 31.2 46 0.001 28.0 2.7 32 26-60 1-33 (343)
66 COG0846 SIR2 NAD-dependent pro 31.0 4.2 9E-05 33.5 -3.5 34 24-57 120-155 (250)
67 PF04810 zf-Sec23_Sec24: Sec23 30.5 15 0.00033 21.7 -0.2 31 26-56 2-32 (40)
68 PF10083 DUF2321: Uncharacteri 30.5 18 0.00039 28.3 0.1 35 24-58 37-78 (158)
69 PRK06393 rpoE DNA-directed RNA 29.7 32 0.0007 23.0 1.3 17 26-42 17-34 (64)
70 PF03604 DNA_RNApol_7kD: DNA d 29.6 19 0.00041 20.8 0.1 24 28-56 2-25 (32)
71 PF13297 Telomere_Sde2_2: Telo 28.0 64 0.0014 21.4 2.4 25 96-120 18-44 (60)
72 KOG1597 Transcription initiati 27.8 24 0.00053 30.2 0.5 33 28-61 2-34 (308)
73 smart00834 CxxC_CXXC_SSSS Puta 27.5 18 0.00038 20.6 -0.3 28 28-56 7-34 (41)
74 PRK00241 nudC NADH pyrophospha 26.6 23 0.00051 28.8 0.2 34 23-60 96-129 (256)
75 TIGR01031 rpmF_bact ribosomal 26.6 14 0.00031 23.6 -0.8 25 24-57 24-48 (55)
76 PF08273 Prim_Zn_Ribbon: Zinc- 26.2 22 0.00047 21.6 -0.1 28 27-54 4-32 (40)
77 COG1405 SUA7 Transcription ini 26.0 23 0.00049 29.7 0.0 11 24-34 18-28 (285)
78 PHA00626 hypothetical protein 26.0 16 0.00035 24.2 -0.7 33 28-61 2-36 (59)
79 PF07754 DUF1610: Domain of un 26.0 28 0.0006 19.1 0.3 23 29-55 1-23 (24)
80 PF14227 UBN2_2: gag-polypepti 25.4 57 0.0012 22.5 2.0 26 99-124 52-77 (119)
81 cd07169 NR_DBD_GCNF_like DNA-b 25.3 65 0.0014 22.3 2.2 34 25-63 5-38 (90)
82 PRK01110 rpmF 50S ribosomal pr 25.0 21 0.00045 23.3 -0.3 23 26-58 27-49 (60)
83 cd07168 NR_DBD_DHR4_like DNA-b 24.9 69 0.0015 22.2 2.3 34 25-63 5-38 (90)
84 COG5349 Uncharacterized protei 24.7 23 0.0005 26.7 -0.2 36 24-62 19-54 (126)
85 PHA02942 putative transposase; 23.4 41 0.00088 29.1 1.1 29 23-56 322-350 (383)
86 PF09698 GSu_C4xC__C2xCH: Geob 23.1 46 0.00099 19.4 1.0 18 34-54 18-35 (36)
87 PF10058 DUF2296: Predicted in 22.4 40 0.00086 21.5 0.6 40 17-56 13-52 (54)
88 PF02591 DUF164: Putative zinc 22.3 20 0.00044 22.4 -0.8 29 26-56 22-54 (56)
89 PRK14559 putative protein seri 22.0 80 0.0017 29.5 2.7 39 21-60 10-53 (645)
90 cd06968 NR_DBD_ROR DNA-binding 21.2 79 0.0017 22.1 2.0 33 26-63 5-37 (95)
91 cd07160 NR_DBD_LXR DNA-binding 21.0 89 0.0019 22.2 2.3 33 26-63 18-50 (101)
92 PHA02998 RNA polymerase subuni 20.7 26 0.00056 28.2 -0.6 35 25-60 142-183 (195)
93 PF10966 DUF2768: Protein of u 20.6 47 0.001 21.8 0.7 15 114-128 6-20 (58)
94 smart00440 ZnF_C2C2 C2C2 Zinc 20.5 14 0.0003 22.0 -1.7 31 28-58 2-38 (40)
95 COG2331 Uncharacterized protei 20.5 35 0.00076 23.9 0.1 35 26-63 12-48 (82)
96 PF12553 DUF3742: Protein of u 20.1 38 0.00081 21.8 0.2 9 38-46 34-42 (54)
97 TIGR00244 transcriptional regu 20.1 39 0.00085 26.0 0.3 35 28-62 2-42 (147)
98 TIGR01562 FdhE formate dehydro 20.0 41 0.00089 28.5 0.4 46 24-69 182-231 (305)
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=99.75 E-value=4.8e-19 Score=114.39 Aligned_cols=50 Identities=44% Similarity=0.991 Sum_probs=44.3
Q ss_pred ccccCCCCCCCcccCCCCCCCCcchHHHHHHHHhccccccCCCc-chhhhh
Q 033001 28 SCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKKLALLGRDK-GRAQKR 77 (129)
Q Consensus 28 ~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~~~rp~~~~k-~~~~~r 77 (129)
.|+||++++||+||+||.+..+|||||||||++++..||..+.. +.+..+
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~~~~~~~~ 51 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRKKDQIKRR 51 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCcccccccc
Confidence 59999999999999999888999999999999999999999877 444433
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.70 E-value=8.7e-18 Score=107.54 Aligned_cols=48 Identities=50% Similarity=1.024 Sum_probs=43.5
Q ss_pred CCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHhccc-cccCCCcc
Q 033001 25 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKKL-ALLGRDKG 72 (129)
Q Consensus 25 ~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~~~-rp~~~~k~ 72 (129)
....|+||++++||+||++|.|+..|||||||||++++.. ||..+.+.
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 4679999999999999999999889999999999999998 88877653
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=7.9e-17 Score=96.14 Aligned_cols=35 Identities=60% Similarity=1.277 Sum_probs=28.6
Q ss_pred cccCCCCCCCcccCCCCCCCCcchHHHHHHHHhcc
Q 033001 29 CIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKK 63 (129)
Q Consensus 29 C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~~ 63 (129)
|++|+|++||+||++|.|+.+|||+|||||+++++
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 89999999999999999977799999999999976
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=99.05 E-value=8.4e-11 Score=89.02 Aligned_cols=53 Identities=47% Similarity=0.986 Sum_probs=47.7
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHhccccccCCCcchhhhhh
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKKLALLGRDKGRAQKRK 78 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~~~rp~~~~k~~~~~r~ 78 (129)
...|.+|+++.||+||+++.|++.+|||||++|+++...|++...+..+..+.
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~~ 251 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPRN 251 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCccccccccCccccccc
Confidence 58999999999999999999999999999999999987788888877776664
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.96 E-value=2.5e-10 Score=100.93 Aligned_cols=62 Identities=27% Similarity=0.577 Sum_probs=54.2
Q ss_pred CCCCCCCCCCcccccCCCCCCCcccCCCC-----CCCCcchHHHHHHHHhcccc-ccCCCcchhhhhhh
Q 033001 17 PPAGTFNEMNKSCIDCHTTRTPLWRGGPA-----GPRSLCNACGIRYRKTKKLA-LLGRDKGRAQKRKR 79 (129)
Q Consensus 17 ~~~~~~~~~~~~C~~C~tt~Tp~WRrgp~-----G~~~LCNaCGl~~~k~~~~r-p~~~~k~~~~~r~r 79 (129)
+.....+....+|.||.|+.||+|||+.. | .+||||||||++.|++.| |+.++.+.+.++.+
T Consensus 149 ~n~~~~s~~~~vc~Nc~t~stPlwrR~~~~~s~~~-n~lcnaCgl~~klhg~~r~P~t~ks~~~ks~~~ 216 (498)
T COG5641 149 NNQSDNSNQPHVCSNCKTTSTPLWRRASSESSLPG-NNLCNACGLYLKLHGSPRAPISLKSDSIKSRSS 216 (498)
T ss_pred CCccccccccchhccccccCCccccccccccccCC-ccccccccccccccCCcCCCccccccccccccc
Confidence 33444555566999999999999999998 6 799999999999999999 99999999988885
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=93.93 E-value=0.057 Score=48.82 Aligned_cols=40 Identities=30% Similarity=0.636 Sum_probs=34.0
Q ss_pred CCCcccccCCCCCCCcc--cCCCCCCCCcchHHHHHHHHhcc
Q 033001 24 EMNKSCIDCHTTRTPLW--RGGPAGPRSLCNACGIRYRKTKK 63 (129)
Q Consensus 24 ~~~~~C~~C~tt~Tp~W--Rrgp~G~~~LCNaCGl~~~k~~~ 63 (129)
...+.|.+|+|++.-.| ..+|+-...||-.|=+||+|.+-
T Consensus 384 ~~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKygG 425 (693)
T KOG3554|consen 384 QDGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYGG 425 (693)
T ss_pred CCCCcccccccccccceeccCCCCccchhhHHHHHHHHHhcC
Confidence 34789999999999999 56666667899999999999865
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=93.26 E-value=0.037 Score=49.65 Aligned_cols=53 Identities=28% Similarity=0.336 Sum_probs=42.9
Q ss_pred CcccccCCC-CCCCcccCCCCCCCCcchHHHHHHHHhccccccCCCcchhhhhh
Q 033001 26 NKSCIDCHT-TRTPLWRGGPAGPRSLCNACGIRYRKTKKLALLGRDKGRAQKRK 78 (129)
Q Consensus 26 ~~~C~~C~t-t~Tp~WRrgp~G~~~LCNaCGl~~~k~~~~rp~~~~k~~~~~r~ 78 (129)
...|.+|.+ +.||.||+...-.-++||+||++.+.++..+|+..+.+...++.
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d~n~~~~ 350 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPNSKRS 350 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCCcccccccCCCCChhhhhh
Confidence 556777777 77999988876557999999999999999999988666665533
No 8
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=82.53 E-value=0.25 Score=29.14 Aligned_cols=29 Identities=31% Similarity=0.575 Sum_probs=14.2
Q ss_pred cccccCCCCCCCcccCCCCCCCCcchHHH
Q 033001 27 KSCIDCHTTRTPLWRGGPAGPRSLCNACG 55 (129)
Q Consensus 27 ~~C~~C~tt~Tp~WRrgp~G~~~LCNaCG 55 (129)
+.|.+||..-+..-=.|.+-...+|.+||
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACG 29 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTT
T ss_pred CccccccChhhhhcCCCCCccceECCCCC
Confidence 46999998753332235555567999998
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=80.21 E-value=1.6 Score=31.31 Aligned_cols=37 Identities=32% Similarity=0.546 Sum_probs=26.3
Q ss_pred CCCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHhc
Q 033001 24 EMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTK 62 (129)
Q Consensus 24 ~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~ 62 (129)
...+.|++|+... |.|-.-.-| -.||-.|.-.++..+
T Consensus 11 ~~N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~lg 47 (116)
T PF01412_consen 11 PGNKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRSLG 47 (116)
T ss_dssp TTCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHHHT
T ss_pred cCcCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHHhc
Confidence 4468999999555 599999999 899999988777766
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=80.05 E-value=1.8 Score=30.88 Aligned_cols=45 Identities=31% Similarity=0.509 Sum_probs=35.1
Q ss_pred CCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHhcc----ccccCCCc
Q 033001 25 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKK----LALLGRDK 71 (129)
Q Consensus 25 ~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~~----~rp~~~~k 71 (129)
....|++|+. .-|.|-.-..| -.+|-.|.-..+..+. .+.+.|++
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 3678999998 45999999899 7899999887777654 35555554
No 11
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=78.41 E-value=0.53 Score=35.59 Aligned_cols=30 Identities=30% Similarity=0.566 Sum_probs=22.6
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
--.|..|+.++|-+=+.+..- -.-|+|||-
T Consensus 102 yVlC~~C~spdT~l~k~~r~~-~l~C~ACGa 131 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGRIW-VLKCEACGA 131 (138)
T ss_pred cEECCCCCCCCcEEEEcCCeE-EEEcccCCC
Confidence 357999999999997753322 346999995
No 12
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=77.20 E-value=0.62 Score=35.01 Aligned_cols=29 Identities=28% Similarity=0.656 Sum_probs=22.1
Q ss_pred cccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 27 KSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 27 ~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
-.|..|+.++|-+-+.+..- -.-|+|||-
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 57999999999998753321 246999995
No 13
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=76.44 E-value=0.68 Score=33.70 Aligned_cols=29 Identities=28% Similarity=0.496 Sum_probs=21.8
Q ss_pred cccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 27 KSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 27 ~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
-.|..|+.++|-+=+.+..- -.-|+|||-
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 57999999999998763222 235999983
No 14
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=73.30 E-value=1.7 Score=37.08 Aligned_cols=47 Identities=30% Similarity=0.494 Sum_probs=35.4
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHhccc----cccCCCc
Q 033001 23 NEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKKL----ALLGRDK 71 (129)
Q Consensus 23 ~~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~~~----rp~~~~k 71 (129)
....+.|++|+++. |.|-.-.-| ..||-.|-=-.|.-|.+ |-+.||.
T Consensus 17 ~~~Nk~CaDCga~~-P~W~S~nlG-vfiCi~CagvHRsLGvhiS~VKSitLD~ 67 (319)
T COG5347 17 DSSNKKCADCGAPN-PTWASVNLG-VFLCIDCAGVHRSLGVHISKVKSLTLDN 67 (319)
T ss_pred ccccCccccCCCCC-CceEecccC-eEEEeecchhhhccccceeeeeeeeccc
Confidence 44578999999999 999999999 89999996544443332 4455554
No 15
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=72.03 E-value=0.97 Score=35.79 Aligned_cols=29 Identities=28% Similarity=0.515 Sum_probs=22.2
Q ss_pred cccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 27 KSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 27 ~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
-.|..|+.++|-+-+.+..- ..-|+|||-
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 57999999999997764222 246999996
No 16
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=71.17 E-value=2.6 Score=39.34 Aligned_cols=42 Identities=24% Similarity=0.517 Sum_probs=32.7
Q ss_pred CCCCCCCCCCCcccccCCCCCCCcccCCCCC---CCCcchHHHHH
Q 033001 16 SPPAGTFNEMNKSCIDCHTTRTPLWRGGPAG---PRSLCNACGIR 57 (129)
Q Consensus 16 ~~~~~~~~~~~~~C~~C~tt~Tp~WRrgp~G---~~~LCNaCGl~ 57 (129)
+..++.-...+-.|..|.|.-||.|+.-+.+ .+++|.+|---
T Consensus 452 q~~at~~a~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtS 496 (706)
T KOG3740|consen 452 QGKATTLATEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTS 496 (706)
T ss_pred ccccccccCCchhhhhcccccccccccccccCcchHHHHHhhhhh
Confidence 3345555666899999999999999887665 45799999653
No 17
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=68.43 E-value=3.6 Score=36.13 Aligned_cols=46 Identities=28% Similarity=0.484 Sum_probs=35.8
Q ss_pred CCCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHhccc----cccCCCc
Q 033001 24 EMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKKL----ALLGRDK 71 (129)
Q Consensus 24 ~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~~~----rp~~~~k 71 (129)
...+.|.+|+... |.|-.-..| ..+|..|.=..|..+.+ |.+.|++
T Consensus 20 PgNk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRsLGvHISfVRSltLD~ 69 (395)
T PLN03114 20 SDNKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRSLGVHISFVRSTNLDS 69 (395)
T ss_pred cCCCcCccCCCCC-CCceeeccc-eeehhhhhHhhccCCCCCceeecccCCC
Confidence 3578899999875 999999999 79999997766665542 5666664
No 18
>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=68.17 E-value=9.6 Score=25.56 Aligned_cols=45 Identities=22% Similarity=0.463 Sum_probs=33.7
Q ss_pred CCCcccccCCCCCCCc--ccCC-CCCCCCcchHHHHHHHHhccccccC
Q 033001 24 EMNKSCIDCHTTRTPL--WRGG-PAGPRSLCNACGIRYRKTKKLALLG 68 (129)
Q Consensus 24 ~~~~~C~~C~tt~Tp~--WRrg-p~G~~~LCNaCGl~~~k~~~~rp~~ 68 (129)
.....|..|..+.|-- .-.. ..-|..+|-+|--||-..+..|-+-
T Consensus 3 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVP 50 (63)
T PF02701_consen 3 EQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVP 50 (63)
T ss_pred ccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCc
Confidence 4567899999998854 2222 2456789999999999999877653
No 19
>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=67.49 E-value=1.8 Score=26.46 Aligned_cols=25 Identities=44% Similarity=1.070 Sum_probs=19.1
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHH
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACG 55 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCG 55 (129)
...|..| .||+.| ..+| ..+|-+|+
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 4578888 589999 4466 68999885
No 20
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=65.73 E-value=1.4 Score=32.62 Aligned_cols=29 Identities=31% Similarity=0.574 Sum_probs=22.5
Q ss_pred cccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 27 KSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 27 ~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
-.|..|+.++|-+=..+..- -.-|+|||-
T Consensus 94 VlC~~C~spdT~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCC-EEEETTTSC
T ss_pred EEcCCCCCCccEEEEcCCEE-EEEecccCC
Confidence 46999999999998774433 356999983
No 21
>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=65.73 E-value=1.8 Score=25.95 Aligned_cols=26 Identities=23% Similarity=0.782 Sum_probs=17.2
Q ss_pred ccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 28 SCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 28 ~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
.|.+|+.+. ..+- ...| ..+|..||+
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 688999876 3332 3345 679999996
No 22
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=62.74 E-value=3.8 Score=37.99 Aligned_cols=46 Identities=24% Similarity=0.438 Sum_probs=32.7
Q ss_pred CCCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHH-hccccccCCCc
Q 033001 24 EMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRK-TKKLALLGRDK 71 (129)
Q Consensus 24 ~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k-~~~~rp~~~~k 71 (129)
...+.|.+|+... |.|-.-..| -.+|-.|.=..|. ..+.+.+.|++
T Consensus 21 PgNk~CADCgs~~-P~WASiNlG-IFICi~CSGIHRsLGhRVKSLSLDk 67 (648)
T PLN03119 21 PPNRRCINCNSLG-PQYVCTTFW-TFVCMACSGIHREFTHRVKSVSMSK 67 (648)
T ss_pred cCCCccccCCCCC-CCceeeccc-eEEeccchhhhccCCceeeccccCC
Confidence 4568999999876 999999999 7899999533333 22335555554
No 23
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=61.47 E-value=1.4 Score=29.59 Aligned_cols=33 Identities=18% Similarity=0.297 Sum_probs=24.5
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHHHHH
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRY 58 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~ 58 (129)
.-.|..|.+..|-.|.+-..-+..-|-+||-..
T Consensus 10 GA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~ 42 (66)
T COG3529 10 GAVCPACQAQDTLAMWRENNVEIVECVKCGHHM 42 (66)
T ss_pred cCCCcccchhhHHHHHHhcCCceEehhhcchHh
Confidence 457999999999665444444477899999855
No 24
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=60.04 E-value=5.9 Score=21.45 Aligned_cols=23 Identities=22% Similarity=0.660 Sum_probs=15.4
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
.+.|.+||+... .+ ..+|..||-
T Consensus 2 ~~~Cp~Cg~~~~-------~~-~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEID-------PD-AKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCC-------cc-cccChhhCC
Confidence 467888988432 23 458888874
No 25
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=59.35 E-value=6.2 Score=26.33 Aligned_cols=38 Identities=29% Similarity=0.432 Sum_probs=27.5
Q ss_pred CCCCCCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHhcc
Q 033001 21 TFNEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKK 63 (129)
Q Consensus 21 ~~~~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~~ 63 (129)
.+....-.|.+|+.-.|-. .+...-|-.||-+...+.+
T Consensus 15 r~~~miYiCgdC~~en~lk-----~~D~irCReCG~RIlyKkR 52 (62)
T KOG3507|consen 15 RTATMIYICGDCGQENTLK-----RGDVIRCRECGYRILYKKR 52 (62)
T ss_pred CcccEEEEecccccccccc-----CCCcEehhhcchHHHHHHH
Confidence 3455577899999998876 4546789999976554433
No 26
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=58.72 E-value=2.5 Score=27.47 Aligned_cols=25 Identities=24% Similarity=0.683 Sum_probs=18.9
Q ss_pred CCCcccccCCCCCCCcccCCCCCCCCcchHHHHH
Q 033001 24 EMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIR 57 (129)
Q Consensus 24 ~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~ 57 (129)
...-.|.+||...-| +.+|..||.|
T Consensus 25 ~~l~~C~~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 25 PGLVECPNCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred CcceECCCCCCccCC---------eEECCCCCcC
Confidence 345679999987655 6799999954
No 27
>PLN03131 hypothetical protein; Provisional
Probab=57.39 E-value=5.7 Score=37.22 Aligned_cols=46 Identities=20% Similarity=0.387 Sum_probs=32.3
Q ss_pred CCCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHh-ccccccCCCc
Q 033001 24 EMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT-KKLALLGRDK 71 (129)
Q Consensus 24 ~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~-~~~rp~~~~k 71 (129)
...+.|.+|+... |.|-.-..| ..+|-.|.=..|.. -+.+.+.|++
T Consensus 21 PgNk~CADCga~~-P~WASiNlG-IFICi~CSGIHRsLghRVKSVTLD~ 67 (705)
T PLN03131 21 PPNRRCINCNSLG-PQFVCTNFW-TFICMTCSGIHREFTHRVKSVSMSK 67 (705)
T ss_pred cCCCccccCCCCC-CCeeEeccc-eEEchhchhhhcccCcccccccCCC
Confidence 4568999999865 999998899 78999995433332 2335555544
No 28
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=54.78 E-value=3 Score=29.99 Aligned_cols=36 Identities=14% Similarity=0.235 Sum_probs=23.3
Q ss_pred CCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHh
Q 033001 25 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 61 (129)
Q Consensus 25 ~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~ 61 (129)
..-.|.+|+...-+. ..+...++..|..||.|+-..
T Consensus 20 t~f~CP~Cge~~v~v-~~~k~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 20 KIFECPRCGKVSISV-KIKKNIAIITCGNCGLYTEFE 55 (99)
T ss_pred cEeECCCCCCeEeee-ecCCCcceEECCCCCCccCEE
Confidence 466799999532222 112234478999999987653
No 29
>PRK00420 hypothetical protein; Validated
Probab=54.11 E-value=5.3 Score=29.36 Aligned_cols=30 Identities=30% Similarity=0.633 Sum_probs=22.2
Q ss_pred CCcccccCCCCCCCcccCCCCCCCCcchHHHHHHH
Q 033001 25 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYR 59 (129)
Q Consensus 25 ~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~ 59 (129)
....|..|| +|+.|- ..| +.+|-.||-.+.
T Consensus 22 l~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCC---Ccceec-CCC-ceECCCCCCeee
Confidence 347888898 677774 456 789999997443
No 30
>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=53.39 E-value=6.3 Score=25.27 Aligned_cols=31 Identities=19% Similarity=0.505 Sum_probs=22.3
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCCCcchHHHHH
Q 033001 23 NEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIR 57 (129)
Q Consensus 23 ~~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~ 57 (129)
......|..||...-. ...+....|..||..
T Consensus 25 ~~TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 25 AYTSQTCPRCGHRNKK----RRSGRVFTCPNCGFE 55 (69)
T ss_pred CCCccCccCccccccc----ccccceEEcCCCCCE
Confidence 3367889999998755 334445789999873
No 31
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=53.30 E-value=2.8 Score=28.38 Aligned_cols=34 Identities=21% Similarity=0.372 Sum_probs=26.0
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHHHHHH
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYR 59 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~ 59 (129)
.-.|..|.+..|-+|....+-...-|-+||..-.
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred CccCCCCcCccEEEEEEeCCceEEEecCCCCeec
Confidence 4579999999998866555554678999997443
No 32
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=52.56 E-value=7.5 Score=35.45 Aligned_cols=31 Identities=23% Similarity=0.440 Sum_probs=21.2
Q ss_pred cccccCCCCCCCcccCCCCCCCCcchHHHHHHHH
Q 033001 27 KSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRK 60 (129)
Q Consensus 27 ~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k 60 (129)
..|.||+.+.=-. +++.....|++||.-.-.
T Consensus 1 ~~C~~C~~s~fe~---d~a~g~~~C~~CG~v~E~ 31 (521)
T KOG1598|consen 1 MVCKNCGGSNFER---DEATGNLYCTACGTVLEY 31 (521)
T ss_pred CcCCCCCCCCccc---ccccCCceeccccceeec
Confidence 4799999876433 444337899999975443
No 33
>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=52.21 E-value=13 Score=24.43 Aligned_cols=31 Identities=35% Similarity=0.717 Sum_probs=23.4
Q ss_pred CCcccccCCCCCCCcccCCCCCCCCcc-hHHHHHHHHhcc
Q 033001 25 MNKSCIDCHTTRTPLWRGGPAGPRSLC-NACGIRYRKTKK 63 (129)
Q Consensus 25 ~~~~C~~C~tt~Tp~WRrgp~G~~~LC-NaCGl~~~k~~~ 63 (129)
..+.|.+||.+.-| . ..+| ..|+--|.++++
T Consensus 2 ~HkHC~~CG~~Ip~-------~-~~fCS~~C~~~~~k~qk 33 (59)
T PF09889_consen 2 PHKHCPVCGKPIPP-------D-ESFCSPKCREEYRKRQK 33 (59)
T ss_pred CCCcCCcCCCcCCc-------c-hhhhCHHHHHHHHHHHH
Confidence 35789999976544 2 6799 599998887755
No 34
>PF15396 FAM60A: Protein Family FAM60A
Probab=50.96 E-value=9.7 Score=31.04 Aligned_cols=22 Identities=32% Similarity=0.614 Sum_probs=17.1
Q ss_pred CcchHHHHHHHHhccccccCCCc
Q 033001 49 SLCNACGIRYRKTKKLALLGRDK 71 (129)
Q Consensus 49 ~LCNaCGl~~~k~~~~rp~~~~k 71 (129)
.+||||-|..++-++ .|.+.++
T Consensus 50 eICNACVLLVKRwKK-LP~Gs~r 71 (213)
T PF15396_consen 50 EICNACVLLVKRWKK-LPPGSKR 71 (213)
T ss_pred hhhHHHHHHHHHHhh-CCCCccc
Confidence 599999999988766 5666544
No 35
>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=50.47 E-value=7.2 Score=22.99 Aligned_cols=27 Identities=30% Similarity=0.707 Sum_probs=20.4
Q ss_pred CCcccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 25 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 25 ~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
....|..|+.. |-...+| ...|..||-
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 5556678 789999984
No 36
>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=49.45 E-value=8.9 Score=22.94 Aligned_cols=29 Identities=21% Similarity=0.602 Sum_probs=21.2
Q ss_pred CcccccCCCCCCCcccCCC-CCCCCcchHHH
Q 033001 26 NKSCIDCHTTRTPLWRGGP-AGPRSLCNACG 55 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp-~G~~~LCNaCG 55 (129)
...|..|+.+..=.|..-. .| ..+|+.||
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 4579999998876675533 35 68999996
No 37
>COG3952 Predicted membrane protein [Function unknown]
Probab=49.05 E-value=4.2 Score=30.05 Aligned_cols=20 Identities=30% Similarity=0.413 Sum_probs=14.8
Q ss_pred cccCCCCCCCCcchHHHHHHHH
Q 033001 39 LWRGGPAGPRSLCNACGIRYRK 60 (129)
Q Consensus 39 ~WRrgp~G~~~LCNaCGl~~~k 60 (129)
+||.+|-+ .+|++||++-..
T Consensus 76 i~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHhcchHH--HHHHhhhHHHHH
Confidence 36777766 699999986543
No 38
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=48.86 E-value=7.1 Score=33.06 Aligned_cols=28 Identities=36% Similarity=0.820 Sum_probs=25.5
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHH
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACG 55 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCG 55 (129)
.+.|++|++. .|.|-.-.-| ..+|-.|-
T Consensus 25 N~~CADC~a~-~P~WaSwnlG-vFiC~~C~ 52 (287)
T KOG0703|consen 25 NKVCADCGAK-GPRWASWNLG-VFICLRCA 52 (287)
T ss_pred cCcccccCCC-CCCeEEeecC-eEEEeecc
Confidence 7899999999 9999998899 78999994
No 39
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=47.53 E-value=7.9 Score=32.22 Aligned_cols=28 Identities=21% Similarity=0.703 Sum_probs=14.6
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
...|.+|+.+ ..... -..| ..+|..||+
T Consensus 11 ~~~Cp~Cg~~-~iv~d-~~~G-e~vC~~CG~ 38 (310)
T PRK00423 11 KLVCPECGSD-KLIYD-YERG-EIVCADCGL 38 (310)
T ss_pred CCcCcCCCCC-CeeEE-CCCC-eEeecccCC
Confidence 3457777642 22222 2345 566777765
No 40
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=47.28 E-value=6.1 Score=33.32 Aligned_cols=35 Identities=23% Similarity=0.423 Sum_probs=26.5
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHh
Q 033001 23 NEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 61 (129)
Q Consensus 23 ~~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~ 61 (129)
....+.|..||+...|. ..|-...|+.||..+.-.
T Consensus 108 ~~~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~fPR 142 (279)
T COG2816 108 YRSHRFCGRCGTKTYPR----EGGWARVCPKCGHEHFPR 142 (279)
T ss_pred HhhCcCCCCCCCcCccc----cCceeeeCCCCCCccCCC
Confidence 34578999999998875 344467999999876543
No 41
>PF12773 DZR: Double zinc ribbon
Probab=44.83 E-value=13 Score=22.34 Aligned_cols=29 Identities=28% Similarity=0.657 Sum_probs=16.6
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 23 NEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 23 ~~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
......|.+||+.-. .+......|..||-
T Consensus 9 ~~~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP-----PPDQSKKICPNCGA 37 (50)
T ss_pred CccccCChhhcCChh-----hccCCCCCCcCCcC
Confidence 344667777777666 22222456666664
No 42
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=44.47 E-value=18 Score=31.26 Aligned_cols=30 Identities=23% Similarity=0.602 Sum_probs=22.6
Q ss_pred CCCcccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 24 EMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 24 ~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
.....|.|||...|+-. ++|..-+|-+||-
T Consensus 313 ~k~nfc~ncG~~~t~~~---~ng~a~fcp~cgq 342 (345)
T COG4260 313 AKLNFCLNCGCGTTADF---DNGKAKFCPECGQ 342 (345)
T ss_pred cccccccccCcccccCC---ccchhhhChhhcC
Confidence 45669999998888863 4554559999984
No 43
>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=42.76 E-value=5.3 Score=26.43 Aligned_cols=33 Identities=18% Similarity=0.274 Sum_probs=24.1
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHHHHH
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRY 58 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~ 58 (129)
.-.|..|....|-+|-....-...-|-.||-.-
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred cccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 457999999999775544443367899999743
No 44
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=41.65 E-value=16 Score=19.46 Aligned_cols=7 Identities=43% Similarity=1.450 Sum_probs=4.0
Q ss_pred CcchHHH
Q 033001 49 SLCNACG 55 (129)
Q Consensus 49 ~LCNaCG 55 (129)
.+|..||
T Consensus 14 ~fC~~CG 20 (23)
T PF13240_consen 14 KFCPNCG 20 (23)
T ss_pred cchhhhC
Confidence 4566665
No 45
>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=39.19 E-value=8.3 Score=23.09 Aligned_cols=28 Identities=21% Similarity=0.412 Sum_probs=16.8
Q ss_pred ccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 28 SCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 28 ~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
.|..||..-+-+..-.. .....|-+||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 57778866554443333 33567888774
No 46
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=38.04 E-value=14 Score=33.11 Aligned_cols=39 Identities=31% Similarity=0.602 Sum_probs=31.3
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHhcc
Q 033001 23 NEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKK 63 (129)
Q Consensus 23 ~~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~~ 63 (129)
....++|++|+.. -|.|-.-+.| -.||--|---.|--|+
T Consensus 20 ~~~NKvCFDCgAk-nPtWaSVTYG-IFLCiDCSAvHRnLGV 58 (454)
T KOG0706|consen 20 QSENKVCFDCGAK-NPTWASVTYG-IFLCIDCSAVHRNLGV 58 (454)
T ss_pred CCCCceecccCCC-CCCceeecce-EEEEEecchhhhcccc
Confidence 3457899999975 6999999999 8999999875555444
No 47
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=37.94 E-value=10 Score=23.28 Aligned_cols=28 Identities=21% Similarity=0.432 Sum_probs=19.9
Q ss_pred ccccCCCCCCCcccCCCCCCCCcchHHHHHHHH
Q 033001 28 SCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRK 60 (129)
Q Consensus 28 ~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k 60 (129)
.|.+||...+.. .+...-|..||-+.-.
T Consensus 4 ~C~~Cg~~~~~~-----~~~~irC~~CG~rIly 31 (44)
T smart00659 4 ICGECGRENEIK-----SKDVVRCRECGYRILY 31 (44)
T ss_pred ECCCCCCEeecC-----CCCceECCCCCceEEE
Confidence 699999987765 2225789999965443
No 48
>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=37.27 E-value=4.8 Score=22.65 Aligned_cols=27 Identities=30% Similarity=0.731 Sum_probs=14.9
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
.+.|..||....+. +.|-...|.+||.
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 56899999877665 2344568888886
No 49
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=35.36 E-value=20 Score=23.72 Aligned_cols=16 Identities=19% Similarity=0.553 Sum_probs=13.8
Q ss_pred cccccCCCCC-CCcccC
Q 033001 27 KSCIDCHTTR-TPLWRG 42 (129)
Q Consensus 27 ~~C~~C~tt~-Tp~WRr 42 (129)
..|.+|+++. |..|..
T Consensus 16 ~~CP~Cgs~~~T~~W~G 32 (61)
T PRK08351 16 DRCPVCGSRDLSDEWFD 32 (61)
T ss_pred CcCCCCcCCcccccccc
Confidence 3699999999 999975
No 50
>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=35.32 E-value=14 Score=29.11 Aligned_cols=28 Identities=32% Similarity=0.767 Sum_probs=22.2
Q ss_pred ccccCCCCCCCcccCCCCCCC--CcchHHH
Q 033001 28 SCIDCHTTRTPLWRGGPAGPR--SLCNACG 55 (129)
Q Consensus 28 ~C~~C~tt~Tp~WRrgp~G~~--~LCNaCG 55 (129)
+|.+||.....++|.-..|.- +-|..||
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~ 31 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCG 31 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccC
Confidence 699999999889988655522 5799996
No 51
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=35.00 E-value=12 Score=22.66 Aligned_cols=26 Identities=31% Similarity=0.563 Sum_probs=18.3
Q ss_pred cccccCCCCCCCcccCCCCCCCCcchHHH
Q 033001 27 KSCIDCHTTRTPLWRGGPAGPRSLCNACG 55 (129)
Q Consensus 27 ~~C~~C~tt~Tp~WRrgp~G~~~LCNaCG 55 (129)
-.|..|+.+ ...|-++ .+ ..-|++|+
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 569999998 5555444 34 57898886
No 52
>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=34.93 E-value=13 Score=22.28 Aligned_cols=31 Identities=26% Similarity=0.589 Sum_probs=18.5
Q ss_pred cccccCCCCCCCcc--cCCCCCCCCcchHHHHHH
Q 033001 27 KSCIDCHTTRTPLW--RGGPAGPRSLCNACGIRY 58 (129)
Q Consensus 27 ~~C~~C~tt~Tp~W--Rrgp~G~~~LCNaCGl~~ 58 (129)
+.|+-||.+.+..= =.||.+ ...|+.|-...
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 57999999886431 256666 68999997643
No 53
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=34.57 E-value=18 Score=28.27 Aligned_cols=29 Identities=21% Similarity=0.572 Sum_probs=24.1
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHH
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACG 55 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCG 55 (129)
...|..||+.....|-.-+.| ..+|..|+
T Consensus 149 l~~C~~Cg~~~~~~~f~~~~g-g~~c~~c~ 177 (247)
T PRK00085 149 LDHCAVCGAPGDHRYFSPKEG-GAVCSECG 177 (247)
T ss_pred hhhHhcCCCCCCceEEecccC-Cccccccc
Confidence 358999999887777777777 78999997
No 54
>KOG4215 consensus Hepatocyte nuclear factor 4 and similar steroid hormone receptors [Transcription]
Probab=34.56 E-value=1e+02 Score=27.49 Aligned_cols=37 Identities=19% Similarity=0.360 Sum_probs=25.9
Q ss_pred CCCCCCCCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHH
Q 033001 19 AGTFNEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRK 60 (129)
Q Consensus 19 ~~~~~~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k 60 (129)
..++....-.|+-||...|-- -.| .+-||.|-=++|+
T Consensus 12 ~~~~s~~~~~CaICGDkaTGK----HYG-A~SCdGCKGFFRR 48 (432)
T KOG4215|consen 12 LQSSSGVAEFCAICGDKATGK----HYG-AISCDGCKGFFRR 48 (432)
T ss_pred cCCcccccchhheeCCccccc----ccc-eeecCcchHHHHH
Confidence 344556788999999988743 356 6789999545443
No 55
>PF14122 YokU: YokU-like protein
Probab=33.90 E-value=7.7 Score=27.55 Aligned_cols=34 Identities=29% Similarity=0.796 Sum_probs=22.1
Q ss_pred ccccCCCCC------CCcccCCC---------CCCCCcchHHHHHHHHhc
Q 033001 28 SCIDCHTTR------TPLWRGGP---------AGPRSLCNACGIRYRKTK 62 (129)
Q Consensus 28 ~C~~C~tt~------Tp~WRrgp---------~G~~~LCNaCGl~~~k~~ 62 (129)
.|..|+..+ |-.| .-| +.|...|+.||+-|.-..
T Consensus 1 ~C~wC~~~~a~~~~~tvyW-eLpdGtraIeI~~tP~i~C~~CgmvYq~d~ 49 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYW-ELPDGTRAIEITDTPAIICSNCGMVYQDDE 49 (87)
T ss_pred CcccccCcccccccceEEE-EcCCCceEEEecCCceeeecCCCcEEehhH
Confidence 388888763 3446 223 344579999999776543
No 56
>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=33.33 E-value=15 Score=22.33 Aligned_cols=28 Identities=21% Similarity=0.528 Sum_probs=17.9
Q ss_pred ccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 28 SCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 28 ~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
.|.+|+..-+ .|+.-.+.....|-.||-
T Consensus 7 ~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFE-VLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeE-EEEecCCCCCCCCCCCCC
Confidence 6888887554 455433333567888886
No 57
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=33.28 E-value=13 Score=28.65 Aligned_cols=31 Identities=26% Similarity=0.453 Sum_probs=24.2
Q ss_pred CCcccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 25 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 25 ~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
.-..|..|+...|++-+.+..- ..-|-|||-
T Consensus 104 ~yv~C~~c~s~dt~l~~~~R~~-~l~c~acGa 134 (151)
T COG1601 104 EYVKCKECGSPDTELIKEERLL-FLKCEACGA 134 (151)
T ss_pred heeEeccCCCCchhhhhhhhhH-hhHHHHhCC
Confidence 3468999999999998874433 357999995
No 58
>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=33.26 E-value=7.3 Score=24.86 Aligned_cols=22 Identities=27% Similarity=0.792 Sum_probs=16.4
Q ss_pred CCcccccCCCCCCCcccCCCCCCCCcchHHH
Q 033001 25 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACG 55 (129)
Q Consensus 25 ~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCG 55 (129)
....|.+||... -++.+|..||
T Consensus 25 ~l~~c~~cg~~~---------~~H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPK---------LPHRVCPSCG 46 (56)
T ss_dssp SEEESSSSSSEE---------STTSBCTTTB
T ss_pred ceeeeccCCCEe---------cccEeeCCCC
Confidence 457899999533 2368999999
No 59
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.05 E-value=19 Score=28.29 Aligned_cols=27 Identities=26% Similarity=0.459 Sum_probs=20.5
Q ss_pred CCCCCcccccCCCCCCCcccCCCCCCCCcchHHHHH
Q 033001 22 FNEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIR 57 (129)
Q Consensus 22 ~~~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~ 57 (129)
.......|+.||. ..+....|..||..
T Consensus 305 ~~~tS~~C~~cg~---------~~~r~~~C~~cg~~ 331 (364)
T COG0675 305 PYYTSKTCPCCGH---------LSGRLFKCPRCGFV 331 (364)
T ss_pred CCCCcccccccCC---------ccceeEECCCCCCe
Confidence 4566789999999 33446789999963
No 60
>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=33.03 E-value=11 Score=31.89 Aligned_cols=36 Identities=19% Similarity=0.505 Sum_probs=25.5
Q ss_pred CCCCcccccCCCCCCCcc----cCCCCCCC---CcchHHHHHHH
Q 033001 23 NEMNKSCIDCHTTRTPLW----RGGPAGPR---SLCNACGIRYR 59 (129)
Q Consensus 23 ~~~~~~C~~C~tt~Tp~W----Rrgp~G~~---~LCNaCGl~~~ 59 (129)
......|..|+-...-.| |...++ - +.|..||-+|+
T Consensus 255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEp-mT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 255 VTDLFTCGKCKQKKCTYYQLQTRSADEP-MTTFVTCEECGNRWK 297 (299)
T ss_pred CcccccCCCCCCccceEEEecccCCCCC-CeEEEEcCCCCCeee
Confidence 344689999998887666 333333 3 37999998886
No 61
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=32.95 E-value=21 Score=28.37 Aligned_cols=24 Identities=33% Similarity=0.439 Sum_probs=12.5
Q ss_pred cchhhhhhhhccCC-----CCHH-HHHHHH
Q 033001 95 GISLKAGLMAVGSD-----MGEE-EQAAIL 118 (129)
Q Consensus 95 ~~~~k~~l~~~~r~-----lgee-e~Aa~l 118 (129)
...++.++.++-.. ..|| |+||++
T Consensus 131 ~i~~~~~I~~L~e~Lq~~i~~EefEeAA~i 160 (176)
T COG3880 131 KINPKRKIIALKEALQDLIEREEFEEAAVI 160 (176)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33455555444422 2344 899975
No 62
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=32.15 E-value=20 Score=21.46 Aligned_cols=27 Identities=30% Similarity=0.620 Sum_probs=17.8
Q ss_pred cccccCCCCCCCcccCCCC-CCCCcchHHHH
Q 033001 27 KSCIDCHTTRTPLWRGGPA-GPRSLCNACGI 56 (129)
Q Consensus 27 ~~C~~C~tt~Tp~WRrgp~-G~~~LCNaCGl 56 (129)
+.|..||..-.+. ... .....|..||-
T Consensus 1 ~FCp~Cg~~l~~~---~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 1 KFCPKCGNMLIPK---EGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCCccccc---cCCCCCEEECCcCCC
Confidence 3689998865443 222 23678999994
No 63
>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=31.95 E-value=22 Score=21.00 Aligned_cols=15 Identities=40% Similarity=0.456 Sum_probs=12.3
Q ss_pred HHHHHHHHHhhhccc
Q 033001 113 EQAAILLMSLSYGCL 127 (129)
Q Consensus 113 e~Aa~llm~ls~g~~ 127 (129)
.-+|.|+.++|.|+|
T Consensus 15 a~~a~l~as~s~g~v 29 (33)
T PF09610_consen 15 ALTASLLASGSFGSV 29 (33)
T ss_pred HHHHHHHHceeeeeE
Confidence 467889999999885
No 64
>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=31.50 E-value=19 Score=29.55 Aligned_cols=15 Identities=60% Similarity=0.884 Sum_probs=13.4
Q ss_pred HHHHHHHhhhccccC
Q 033001 115 AAILLMSLSYGCLYA 129 (129)
Q Consensus 115 Aa~llm~ls~g~~~~ 129 (129)
-|.||..+||||+||
T Consensus 120 lAsll~S~sy~Sa~A 134 (246)
T PF10897_consen 120 LASLLISFSYGSAYA 134 (246)
T ss_pred HHHHHHHHHHhHHHH
Confidence 488999999999986
No 65
>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=31.17 E-value=46 Score=27.99 Aligned_cols=32 Identities=28% Similarity=0.377 Sum_probs=22.4
Q ss_pred CcccccCCCCCCCc-ccCCCCCCCCcchHHHHHHHH
Q 033001 26 NKSCIDCHTTRTPL-WRGGPAGPRSLCNACGIRYRK 60 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~-WRrgp~G~~~LCNaCGl~~~k 60 (129)
++.|..|.-+.|-- =.=+.+| +||+|--+..+
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 46899999988632 2223445 99999987654
No 66
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=30.99 E-value=4.2 Score=33.48 Aligned_cols=34 Identities=18% Similarity=0.185 Sum_probs=21.0
Q ss_pred CCCcccccCCCCCCCc-ccCC-CCCCCCcchHHHHH
Q 033001 24 EMNKSCIDCHTTRTPL-WRGG-PAGPRSLCNACGIR 57 (129)
Q Consensus 24 ~~~~~C~~C~tt~Tp~-WRrg-p~G~~~LCNaCGl~ 57 (129)
-....|..|+...... +.+. ..+.-+.|..||-+
T Consensus 120 l~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 155 (250)
T COG0846 120 LKRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGP 155 (250)
T ss_pred eeeeEeCCCcCccchhhhhhhcccCCCCcCccCCCc
Confidence 3467899998765522 2222 22334689999985
No 67
>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=30.51 E-value=15 Score=21.74 Aligned_cols=31 Identities=26% Similarity=0.599 Sum_probs=18.4
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
+.+|..|++---|.-.=...|....||-|+.
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 4679999988877766666666678999985
No 68
>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=30.49 E-value=18 Score=28.27 Aligned_cols=35 Identities=29% Similarity=0.550 Sum_probs=22.9
Q ss_pred CCCcccccCCCCCCCcccC-------CCCCCCCcchHHHHHH
Q 033001 24 EMNKSCIDCHTTRTPLWRG-------GPAGPRSLCNACGIRY 58 (129)
Q Consensus 24 ~~~~~C~~C~tt~Tp~WRr-------gp~G~~~LCNaCGl~~ 58 (129)
.....|.+|++..---|-- ++......|+.||-.|
T Consensus 37 ~tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 37 KTITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHHHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCC
Confidence 3456788888876555532 3334457899999755
No 69
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=29.73 E-value=32 Score=23.01 Aligned_cols=17 Identities=29% Similarity=0.567 Sum_probs=13.2
Q ss_pred CcccccCCCCC-CCcccC
Q 033001 26 NKSCIDCHTTR-TPLWRG 42 (129)
Q Consensus 26 ~~~C~~C~tt~-Tp~WRr 42 (129)
...|.+||++. |+-|..
T Consensus 17 ~~~Cp~Cgs~~~S~~w~G 34 (64)
T PRK06393 17 EKTCPVHGDEKTTTEWFG 34 (64)
T ss_pred CCcCCCCCCCcCCcCcce
Confidence 34899999988 777853
No 70
>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=29.64 E-value=19 Score=20.80 Aligned_cols=24 Identities=25% Similarity=0.553 Sum_probs=14.6
Q ss_pred ccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 28 SCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 28 ~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
.|.+|+....-. .+...-|..||-
T Consensus 2 ~C~~Cg~~~~~~-----~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELK-----PGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BS-----TSSTSSBSSSS-
T ss_pred CCCcCCCeeEcC-----CCCcEECCcCCC
Confidence 488888887722 222467888885
No 71
>PF13297 Telomere_Sde2_2: Telomere stability C-terminal
Probab=27.96 E-value=64 Score=21.39 Aligned_cols=25 Identities=44% Similarity=0.466 Sum_probs=18.8
Q ss_pred chhhhhhhhcc-CCCC-HHHHHHHHHH
Q 033001 96 ISLKAGLMAVG-SDMG-EEEQAAILLM 120 (129)
Q Consensus 96 ~~~k~~l~~~~-r~lg-eee~Aa~llm 120 (129)
+.+|..|+++| ++-| -+|+||-|.-
T Consensus 18 drLK~~L~a~GLKcGGTl~ERA~RLfs 44 (60)
T PF13297_consen 18 DRLKSALMALGLKCGGTLQERAARLFS 44 (60)
T ss_pred HHHHHHHHHcCCccCCCHHHHHHHHHH
Confidence 56788888888 5555 6789988753
No 72
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=27.78 E-value=24 Score=30.22 Aligned_cols=33 Identities=27% Similarity=0.704 Sum_probs=22.7
Q ss_pred ccccCCCCCCCcccCCCCCCCCcchHHHHHHHHh
Q 033001 28 SCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKT 61 (129)
Q Consensus 28 ~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~ 61 (129)
.|..|....-.+--+-..| .++|-.|||-+.-+
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 5788877655555555567 68899998855443
No 73
>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=27.45 E-value=18 Score=20.64 Aligned_cols=28 Identities=32% Similarity=0.596 Sum_probs=17.0
Q ss_pred ccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 28 SCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 28 ~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
.|..|+..-+.. ....++....|-.||-
T Consensus 7 ~C~~Cg~~fe~~-~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVL-QKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEE-EecCCCCCCCCCCCCC
Confidence 688888755432 3222244567888886
No 74
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=26.59 E-value=23 Score=28.81 Aligned_cols=34 Identities=24% Similarity=0.395 Sum_probs=23.7
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHH
Q 033001 23 NEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRK 60 (129)
Q Consensus 23 ~~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k 60 (129)
....+.|..||+..... ..|....|.+||..+.-
T Consensus 96 ~~~~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 96 YRSHRFCGYCGHPMHPS----KTEWAMLCPHCRERYYP 129 (256)
T ss_pred hhcCccccccCCCCeec----CCceeEECCCCCCEECC
Confidence 34578999999976542 34545689999965543
No 75
>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=26.57 E-value=14 Score=23.61 Aligned_cols=25 Identities=24% Similarity=0.675 Sum_probs=17.3
Q ss_pred CCCcccccCCCCCCCcccCCCCCCCCcchHHHHH
Q 033001 24 EMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIR 57 (129)
Q Consensus 24 ~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~ 57 (129)
...-.|.+||...- ++.+|-.||.|
T Consensus 24 p~l~~C~~cG~~~~---------~H~vc~~cG~Y 48 (55)
T TIGR01031 24 PTLVVCPNCGEFKL---------PHRVCPSCGYY 48 (55)
T ss_pred CcceECCCCCCccc---------CeeECCccCeE
Confidence 34566999987543 35799999943
No 76
>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=26.17 E-value=22 Score=21.58 Aligned_cols=28 Identities=14% Similarity=0.345 Sum_probs=15.0
Q ss_pred cccccCCCCCCCc-ccCCCCCCCCcchHH
Q 033001 27 KSCIDCHTTRTPL-WRGGPAGPRSLCNAC 54 (129)
Q Consensus 27 ~~C~~C~tt~Tp~-WRrgp~G~~~LCNaC 54 (129)
..|..|+.+.-=. |..........|+.|
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTT
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCC
Confidence 4688898877655 765333227899999
No 77
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=25.99 E-value=23 Score=29.74 Aligned_cols=11 Identities=27% Similarity=0.573 Sum_probs=6.2
Q ss_pred CCCcccccCCC
Q 033001 24 EMNKSCIDCHT 34 (129)
Q Consensus 24 ~~~~~C~~C~t 34 (129)
....+|.+||.
T Consensus 18 ~ge~VC~~CG~ 28 (285)
T COG1405 18 RGEIVCADCGL 28 (285)
T ss_pred CCeEEeccCCE
Confidence 45556666654
No 78
>PHA00626 hypothetical protein
Probab=25.99 E-value=16 Score=24.17 Aligned_cols=33 Identities=24% Similarity=0.440 Sum_probs=21.4
Q ss_pred ccccCCCCCCCc--ccCCCCCCCCcchHHHHHHHHh
Q 033001 28 SCIDCHTTRTPL--WRGGPAGPRSLCNACGIRYRKT 61 (129)
Q Consensus 28 ~C~~C~tt~Tp~--WRrgp~G~~~LCNaCGl~~~k~ 61 (129)
.|.+|+..+-.. -=+++.. .+.|..||..+-+.
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 78999999877653
No 79
>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=25.95 E-value=28 Score=19.07 Aligned_cols=23 Identities=26% Similarity=0.654 Sum_probs=12.7
Q ss_pred cccCCCCCCCcccCCCCCCCCcchHHH
Q 033001 29 CIDCHTTRTPLWRGGPAGPRSLCNACG 55 (129)
Q Consensus 29 C~~C~tt~Tp~WRrgp~G~~~LCNaCG 55 (129)
|..|+..-.|. .. +....|-.||
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 55666666554 11 3345677766
No 80
>PF14227 UBN2_2: gag-polypeptide of LTR copia-type
Probab=25.37 E-value=57 Score=22.53 Aligned_cols=26 Identities=31% Similarity=0.436 Sum_probs=20.7
Q ss_pred hhhhhhccCCCCHHHHHHHHHHHhhh
Q 033001 99 KAGLMAVGSDMGEEEQAAILLMSLSY 124 (129)
Q Consensus 99 k~~l~~~~r~lgeee~Aa~llm~ls~ 124 (129)
-.+|-++|-.+.++..+.+||..|..
T Consensus 52 ~~~L~~~g~~i~d~~~~~~lL~sLP~ 77 (119)
T PF14227_consen 52 VNQLKSLGVPIDDEDKVIILLSSLPP 77 (119)
T ss_pred HHhhccccccchHHHHHHHHHHcCCH
Confidence 44566667889999999999998864
No 81
>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=25.29 E-value=65 Score=22.30 Aligned_cols=34 Identities=21% Similarity=0.468 Sum_probs=24.8
Q ss_pred CCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHhcc
Q 033001 25 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKK 63 (129)
Q Consensus 25 ~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~~ 63 (129)
....|.-|+...+-.+ .| ...|+||..+|++.-.
T Consensus 5 ~~~~C~VCg~~a~g~h----yG-v~sC~aCk~FFRR~v~ 38 (90)
T cd07169 5 EQRTCLICGDRATGLH----YG-IISCEGCKGFFKRSIC 38 (90)
T ss_pred cCCCCeecCCcCcceE----EC-cceehhhHHHHHHHhc
Confidence 4556999997665543 44 5689999999987643
No 82
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=25.03 E-value=21 Score=23.29 Aligned_cols=23 Identities=9% Similarity=-0.078 Sum_probs=16.0
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHHHHH
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRY 58 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~ 58 (129)
...|.+||+..-| +.+|. ||.|.
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 5678888876544 45788 98653
No 83
>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=24.86 E-value=69 Score=22.15 Aligned_cols=34 Identities=26% Similarity=0.467 Sum_probs=24.3
Q ss_pred CCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHhcc
Q 033001 25 MNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKK 63 (129)
Q Consensus 25 ~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~~ 63 (129)
....|.-|+...+-.+ .| ...|+||..+|++.-.
T Consensus 5 ~~~~C~VCg~~~~g~h----yG-v~sC~aCk~FFRR~v~ 38 (90)
T cd07168 5 SPKLCSICEDKATGLH----YG-IITCEGCKGFFKRTVQ 38 (90)
T ss_pred cCCCCcccCCcCcceE----EC-ceehhhhhHhhhhhhc
Confidence 4556999997655332 34 5789999999987654
No 84
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.68 E-value=23 Score=26.73 Aligned_cols=36 Identities=31% Similarity=0.661 Sum_probs=23.6
Q ss_pred CCCcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHhc
Q 033001 24 EMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTK 62 (129)
Q Consensus 24 ~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~ 62 (129)
+....|.+||.-. +.|. --....-|.|||+-|-.+.
T Consensus 19 Gl~grCP~CGeGr--LF~g-FLK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 19 GLRGRCPRCGEGR--LFRG-FLKVVPACEACGLDYGFAD 54 (126)
T ss_pred HhcCCCCCCCCch--hhhh-hcccCchhhhccccccCCc
Confidence 4567899998543 3332 2233568999999887764
No 85
>PHA02942 putative transposase; Provisional
Probab=23.35 E-value=41 Score=29.06 Aligned_cols=29 Identities=24% Similarity=0.470 Sum_probs=20.7
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 23 NEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 23 ~~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
......|+.||....++ .+....|..||.
T Consensus 322 ~yTSq~Cs~CG~~~~~l-----~~r~f~C~~CG~ 350 (383)
T PHA02942 322 SYSSVSCPKCGHKMVEI-----AHRYFHCPSCGY 350 (383)
T ss_pred CCCCccCCCCCCccCcC-----CCCEEECCCCCC
Confidence 34678999999866432 333578999997
No 86
>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=23.11 E-value=46 Score=19.36 Aligned_cols=18 Identities=33% Similarity=0.981 Sum_probs=13.4
Q ss_pred CCCCCcccCCCCCCCCcchHH
Q 033001 34 TTRTPLWRGGPAGPRSLCNAC 54 (129)
Q Consensus 34 tt~Tp~WRrgp~G~~~LCNaC 54 (129)
...||.|-.+..+. |+.|
T Consensus 18 ~~~~p~W~~~~~~~---C~~C 35 (36)
T PF09698_consen 18 SYTTPTWGSGATTA---CGSC 35 (36)
T ss_pred cccCceeCCCCCCc---cccc
Confidence 34578998887772 8887
No 87
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=22.37 E-value=40 Score=21.49 Aligned_cols=40 Identities=18% Similarity=0.297 Sum_probs=27.1
Q ss_pred CCCCCCCCCCcccccCCCCCCCcccCCCCCCCCcchHHHH
Q 033001 17 PPAGTFNEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGI 56 (129)
Q Consensus 17 ~~~~~~~~~~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl 56 (129)
.+....++...+|.+|....--.=+.....-.+.|-.||-
T Consensus 13 d~~~~~~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 13 DPTSPSNRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred CCccccCceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 3355677789999999987643324455444678888874
No 88
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=22.25 E-value=20 Score=22.36 Aligned_cols=29 Identities=31% Similarity=0.698 Sum_probs=22.1
Q ss_pred CcccccCCCCCCCcc----cCCCCCCCCcchHHHH
Q 033001 26 NKSCIDCHTTRTPLW----RGGPAGPRSLCNACGI 56 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~W----Rrgp~G~~~LCNaCGl 56 (129)
...|..|+..-+|.+ +++ +. -..|..||-
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 469999999999885 555 33 578999984
No 89
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.96 E-value=80 Score=29.49 Aligned_cols=39 Identities=23% Similarity=0.368 Sum_probs=21.9
Q ss_pred CCCCCCcccccCCCCCCCcc-----cCCCCCCCCcchHHHHHHHH
Q 033001 21 TFNEMNKSCIDCHTTRTPLW-----RGGPAGPRSLCNACGIRYRK 60 (129)
Q Consensus 21 ~~~~~~~~C~~C~tt~Tp~W-----Rrgp~G~~~LCNaCGl~~~k 60 (129)
......+.|.+||+.-+..- ..-|.| ..+|..||-+.-.
T Consensus 10 ~n~~~akFC~~CG~~l~~~~Cp~CG~~~~~~-~~fC~~CG~~~~~ 53 (645)
T PRK14559 10 ENPNNNRFCQKCGTSLTHKPCPQCGTEVPVD-EAHCPNCGAETGT 53 (645)
T ss_pred cCCCCCccccccCCCCCCCcCCCCCCCCCcc-cccccccCCcccc
Confidence 34455667777776643110 113445 4699999965443
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=21.19 E-value=79 Score=22.13 Aligned_cols=33 Identities=18% Similarity=0.461 Sum_probs=24.2
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHhcc
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKK 63 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~~ 63 (129)
...|.-|+...+-.+ .| ...|+||..+|++.-.
T Consensus 5 ~~~C~VCg~~~~g~h----yG-v~sC~aC~~FFRR~v~ 37 (95)
T cd06968 5 VIPCKICGDKSSGIH----YG-VITCEGCKGFFRRSQQ 37 (95)
T ss_pred ccCCcccCCcCcceE----EC-ceeehhhHHhhHHhee
Confidence 346999997665543 44 5679999999997654
No 91
>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=21.02 E-value=89 Score=22.23 Aligned_cols=33 Identities=18% Similarity=0.395 Sum_probs=24.0
Q ss_pred CcccccCCCCCCCcccCCCCCCCCcchHHHHHHHHhcc
Q 033001 26 NKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKK 63 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~WRrgp~G~~~LCNaCGl~~~k~~~ 63 (129)
...|.-|+...+-. -.| ...|+||..+|++.-.
T Consensus 18 ~~~C~VCg~~a~g~----hyG-v~sC~aCk~FFRR~v~ 50 (101)
T cd07160 18 NEVCSVCGDKASGF----HYN-VLSCEGCKGFFRRSVI 50 (101)
T ss_pred CCCCeecCCcCcce----EEC-cceehhhhhhhhhccc
Confidence 55799999765533 245 5689999999987643
No 92
>PHA02998 RNA polymerase subunit; Provisional
Probab=20.74 E-value=26 Score=28.18 Aligned_cols=35 Identities=20% Similarity=0.527 Sum_probs=26.9
Q ss_pred CCcccccCCCCCCCcc----cCCCCCCCC---cchHHHHHHHH
Q 033001 25 MNKSCIDCHTTRTPLW----RGGPAGPRS---LCNACGIRYRK 60 (129)
Q Consensus 25 ~~~~C~~C~tt~Tp~W----Rrgp~G~~~---LCNaCGl~~~k 60 (129)
....|..|+-..+-.| |.+.++ .+ .|-.||-.|+-
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEP-mT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEP-PLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCC-ceEEEEcCCCCCccCC
Confidence 4578999999987766 666665 43 79999987763
No 93
>PF10966 DUF2768: Protein of unknown function (DUF2768); InterPro: IPR020076 This entry contains proteins with no known function.
Probab=20.64 E-value=47 Score=21.84 Aligned_cols=15 Identities=40% Similarity=0.310 Sum_probs=12.7
Q ss_pred HHHHHHHHhhhcccc
Q 033001 114 QAAILLMSLSYGCLY 128 (129)
Q Consensus 114 ~Aa~llm~ls~g~~~ 128 (129)
=+|+.||.+|-+++|
T Consensus 6 ~~~iglMfisv~~i~ 20 (58)
T PF10966_consen 6 FGAIGLMFISVILIY 20 (58)
T ss_pred HHHHHHHHHHHHHHH
Confidence 478999999988876
No 94
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=20.49 E-value=14 Score=22.02 Aligned_cols=31 Identities=23% Similarity=0.686 Sum_probs=18.0
Q ss_pred ccccCCCCCCCcc----cCCCCCCC--CcchHHHHHH
Q 033001 28 SCIDCHTTRTPLW----RGGPAGPR--SLCNACGIRY 58 (129)
Q Consensus 28 ~C~~C~tt~Tp~W----Rrgp~G~~--~LCNaCGl~~ 58 (129)
.|..|+-.+.-.| |+..++.- +.|-.||-.|
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 5778886665444 44444421 3577787544
No 95
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.46 E-value=35 Score=23.93 Aligned_cols=35 Identities=23% Similarity=0.592 Sum_probs=23.7
Q ss_pred CcccccCCCCCCCc--ccCCCCCCCCcchHHHHHHHHhcc
Q 033001 26 NKSCIDCHTTRTPL--WRGGPAGPRSLCNACGIRYRKTKK 63 (129)
Q Consensus 26 ~~~C~~C~tt~Tp~--WRrgp~G~~~LCNaCGl~~~k~~~ 63 (129)
.-.|.+|+-..+-+ .+.+| -+.|.+||-.+++.-.
T Consensus 12 ~Y~c~~cg~~~dvvq~~~ddp---lt~ce~c~a~~kk~l~ 48 (82)
T COG2331 12 SYECTECGNRFDVVQAMTDDP---LTTCEECGARLKKLLN 48 (82)
T ss_pred EEeecccchHHHHHHhcccCc---cccChhhChHHHHhhc
Confidence 34799998776533 44444 4589999987776543
No 96
>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=20.12 E-value=38 Score=21.80 Aligned_cols=9 Identities=78% Similarity=1.704 Sum_probs=8.3
Q ss_pred CcccCCCCC
Q 033001 38 PLWRGGPAG 46 (129)
Q Consensus 38 p~WRrgp~G 46 (129)
|.||.||.|
T Consensus 34 ~E~R~G~~G 42 (54)
T PF12553_consen 34 PEWREGPAG 42 (54)
T ss_pred HhheecCCC
Confidence 889999997
No 97
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=20.06 E-value=39 Score=26.05 Aligned_cols=35 Identities=26% Similarity=0.460 Sum_probs=22.7
Q ss_pred ccccCCCCCCCcc--cCCCCCC----CCcchHHHHHHHHhc
Q 033001 28 SCIDCHTTRTPLW--RGGPAGP----RSLCNACGIRYRKTK 62 (129)
Q Consensus 28 ~C~~C~tt~Tp~W--Rrgp~G~----~~LCNaCGl~~~k~~ 62 (129)
.|..|+...|-.- |...+|. .-.|.+||-+|-..-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyE 42 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFE 42 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceee
Confidence 5888888888765 3344442 247888987665443
No 98
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=20.03 E-value=41 Score=28.54 Aligned_cols=46 Identities=20% Similarity=0.377 Sum_probs=33.9
Q ss_pred CCCcccccCCCCCCCcc-cCC--CCCCCC-cchHHHHHHHHhccccccCC
Q 033001 24 EMNKSCIDCHTTRTPLW-RGG--PAGPRS-LCNACGIRYRKTKKLALLGR 69 (129)
Q Consensus 24 ~~~~~C~~C~tt~Tp~W-Rrg--p~G~~~-LCNaCGl~~~k~~~~rp~~~ 69 (129)
.....|--||+.-+--+ |.+ ..|..+ .|+-|+..|+..+...|.--
T Consensus 182 ~~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg 231 (305)
T TIGR01562 182 ESRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCE 231 (305)
T ss_pred CCCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCC
Confidence 45669999999876443 443 456555 59999999999988777643
Done!