Query 032112
Match_columns 147
No_of_seqs 190 out of 794
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 09:45:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032112.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032112hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00320 GATA: GATA zinc finge 99.6 3.7E-16 8.1E-21 95.4 1.5 35 36-70 1-35 (36)
2 cd00202 ZnF_GATA Zinc finger D 99.6 8.7E-16 1.9E-20 101.5 3.3 38 35-72 1-38 (54)
3 smart00401 ZnF_GATA zinc finge 99.6 1.3E-15 2.8E-20 99.7 2.8 40 32-71 2-41 (52)
4 KOG1601 GATA-4/5/6 transcripti 98.9 7.2E-10 1.6E-14 85.9 1.8 37 33-69 199-235 (340)
5 COG5641 GAT1 GATA Zn-finger-co 98.7 4.3E-09 9.3E-14 95.5 1.6 56 27-83 152-214 (498)
6 COG5641 GAT1 GATA Zn-finger-co 95.8 0.0046 9.9E-08 56.7 1.9 92 33-124 297-399 (498)
7 KOG3554 Histone deacetylase co 94.1 0.19 4E-06 46.7 7.2 39 31-69 384-424 (693)
8 PF14803 Nudix_N_2: Nudix N-te 84.1 0.29 6.3E-06 29.6 -0.2 30 34-63 1-30 (34)
9 PF01412 ArfGap: Putative GTPa 81.4 1.3 2.8E-05 32.6 2.4 37 31-69 11-47 (116)
10 COG5347 GTPase-activating prot 78.7 1 2.2E-05 39.3 1.3 39 30-70 17-55 (319)
11 PRK03988 translation initiatio 75.5 0.81 1.8E-05 35.4 -0.2 29 34-63 103-131 (138)
12 TIGR00311 aIF-2beta translatio 74.1 0.94 2E-05 34.9 -0.2 30 34-64 98-127 (133)
13 smart00105 ArfGap Putative GTP 74.0 3 6.4E-05 30.6 2.4 36 32-69 2-37 (112)
14 smart00653 eIF2B_5 domain pres 73.7 1 2.2E-05 33.6 -0.1 29 34-63 81-109 (110)
15 PRK12336 translation initiatio 68.9 1.4 3.1E-05 35.7 -0.3 32 34-66 99-130 (201)
16 cd00202 ZnF_GATA Zinc finger D 68.3 1.1 2.5E-05 29.3 -0.8 27 99-125 26-53 (54)
17 PRK12286 rpmF 50S ribosomal pr 65.9 1.9 4.2E-05 28.7 -0.0 24 33-65 27-50 (57)
18 PF08271 TF_Zn_Ribbon: TFIIB z 65.3 2.2 4.8E-05 26.2 0.1 28 35-65 2-29 (43)
19 PLN03114 ADP-ribosylation fact 65.0 4.5 9.8E-05 36.4 2.1 38 31-70 20-57 (395)
20 KOG0706 Predicted GTPase-activ 64.1 3.3 7.2E-05 37.9 1.1 42 30-73 20-61 (454)
21 KOG3740 Uncharacterized conser 63.1 4.1 8.9E-05 39.0 1.5 40 27-66 456-498 (706)
22 PF01873 eIF-5_eIF-2B: Domain 62.9 2.2 4.7E-05 32.5 -0.3 29 34-63 94-122 (125)
23 COG4260 Membrane protease subu 59.2 7.4 0.00016 34.3 2.3 30 31-63 313-342 (345)
24 COG3529 Predicted nucleic-acid 57.0 2.3 5.1E-05 29.3 -0.9 34 33-66 10-43 (66)
25 smart00778 Prim_Zn_Ribbon Zinc 56.2 6.8 0.00015 24.0 1.2 29 33-62 3-32 (37)
26 KOG0703 Predicted GTPase-activ 53.6 5.3 0.00011 34.7 0.5 35 33-69 25-59 (287)
27 KOG3507 DNA-directed RNA polym 53.6 13 0.00029 25.4 2.3 36 28-68 15-50 (62)
28 PRK14892 putative transcriptio 53.2 4 8.8E-05 30.1 -0.2 36 33-69 21-56 (99)
29 PF01783 Ribosomal_L32p: Ribos 51.1 3.6 7.8E-05 27.0 -0.7 22 32-62 25-46 (56)
30 PF06677 Auto_anti-p27: Sjogre 49.5 7 0.00015 24.4 0.5 24 34-62 18-41 (41)
31 PF06689 zf-C4_ClpX: ClpX C4-t 48.8 8.3 0.00018 23.7 0.7 31 34-65 2-34 (41)
32 PF09526 DUF2387: Probable met 47.8 5.3 0.00012 27.7 -0.3 35 33-67 8-42 (71)
33 PRK00423 tfb transcription ini 47.1 8.2 0.00018 33.0 0.7 30 33-65 11-40 (310)
34 COG3952 Predicted membrane pro 46.0 5.2 0.00011 30.3 -0.6 19 46-66 76-94 (113)
35 PF12773 DZR: Double zinc ribb 45.6 14 0.0003 22.8 1.4 29 31-64 10-38 (50)
36 PF07282 OrfB_Zn_ribbon: Putat 45.5 12 0.00025 24.6 1.1 30 32-65 27-56 (69)
37 PF01096 TFIIS_C: Transcriptio 45.3 2.1 4.5E-05 26.1 -2.4 31 35-65 2-38 (39)
38 cd06955 NR_DBD_VDR DNA-binding 44.1 41 0.00089 24.9 3.9 33 32-69 5-37 (107)
39 TIGR01031 rpmF_bact ribosomal 43.7 6.6 0.00014 25.9 -0.3 23 33-64 26-48 (55)
40 PRK01110 rpmF 50S ribosomal pr 42.4 8.3 0.00018 25.8 0.0 24 33-66 27-50 (60)
41 PF12760 Zn_Tnp_IS1595: Transp 40.8 13 0.00028 23.1 0.7 26 34-62 19-44 (46)
42 PF09723 Zn-ribbon_8: Zinc rib 40.1 9.1 0.0002 23.5 -0.1 28 35-63 7-34 (42)
43 PLN03119 putative ADP-ribosyla 40.0 15 0.00032 35.1 1.2 36 31-68 21-56 (648)
44 PRK08351 DNA-directed RNA poly 39.9 18 0.00039 24.6 1.4 15 35-49 17-32 (61)
45 TIGR02443 conserved hypothetic 38.2 9.5 0.00021 25.9 -0.2 34 33-66 9-42 (59)
46 PF11781 RRN7: RNA polymerase 37.7 16 0.00034 22.1 0.7 27 32-63 7-33 (36)
47 PRK00420 hypothetical protein; 37.4 16 0.00034 27.6 0.8 29 33-66 23-51 (112)
48 smart00659 RPOLCX RNA polymera 35.7 14 0.0003 23.3 0.3 30 35-69 4-33 (44)
49 PRK06393 rpoE DNA-directed RNA 34.4 25 0.00054 24.2 1.4 16 33-48 17-33 (64)
50 PF08273 Prim_Zn_Ribbon: Zinc- 34.1 16 0.00034 22.7 0.3 26 35-61 5-32 (40)
51 PF03604 DNA_RNApol_7kD: DNA d 34.1 9.1 0.0002 22.7 -0.7 26 35-65 2-27 (32)
52 PLN03131 hypothetical protein; 33.8 23 0.0005 34.2 1.5 35 31-67 21-55 (705)
53 smart00440 ZnF_C2C2 C2C2 Zinc 33.8 8.2 0.00018 23.6 -1.0 32 35-66 2-39 (40)
54 cd06966 NR_DBD_CAR DNA-binding 33.3 64 0.0014 23.1 3.4 31 34-69 1-31 (94)
55 COG2816 NPY1 NTP pyrophosphohy 33.0 16 0.00036 31.5 0.4 34 32-69 110-143 (279)
56 PF04810 zf-Sec23_Sec24: Sec23 32.7 19 0.00041 21.8 0.5 31 33-63 2-32 (40)
57 PF10897 DUF2713: Protein of u 31.5 19 0.00042 30.3 0.5 15 133-147 120-134 (246)
58 TIGR01385 TFSII transcription 31.5 14 0.0003 32.0 -0.3 36 31-66 256-297 (299)
59 TIGR02605 CxxC_CxxC_SSSS putat 31.5 18 0.0004 22.5 0.3 28 35-63 7-34 (52)
60 PF15396 FAM60A: Protein Famil 30.8 28 0.00061 29.1 1.3 15 56-70 50-64 (213)
61 PF09297 zf-NADH-PPase: NADH p 30.3 7.3 0.00016 22.5 -1.6 28 33-64 3-30 (32)
62 KOG1598 Transcription initiati 30.0 29 0.00063 32.5 1.4 29 34-65 1-29 (521)
63 PRK00085 recO DNA repair prote 28.4 27 0.00059 28.0 0.9 28 34-62 150-177 (247)
64 smart00661 RPOL9 RNA polymeras 27.9 33 0.00071 21.1 1.0 29 35-66 2-31 (52)
65 KOG0909 Peptide:N-glycanase [P 27.6 25 0.00055 32.6 0.6 34 33-66 161-205 (500)
66 smart00834 CxxC_CXXC_SSSS Puta 26.6 22 0.00047 20.8 0.0 28 35-63 7-34 (41)
67 PF09889 DUF2116: Uncharacteri 26.6 46 0.001 22.3 1.6 30 33-70 3-33 (59)
68 PHA02998 RNA polymerase subuni 26.4 20 0.00042 29.6 -0.3 36 32-67 142-183 (195)
69 cd07162 NR_DBD_PXR DNA-binding 26.2 1.5E+02 0.0032 20.8 4.2 30 35-69 1-30 (87)
70 PF04161 Arv1: Arv1-like famil 25.5 29 0.00063 28.0 0.5 29 35-63 2-32 (208)
71 COG1405 SUA7 Transcription ini 25.3 25 0.00054 30.2 0.1 29 35-66 3-31 (285)
72 COG1601 GCD7 Translation initi 24.7 23 0.00051 27.9 -0.1 31 34-65 106-136 (151)
73 cd02337 ZZ_CBP Zinc finger, ZZ 24.0 54 0.0012 20.2 1.5 30 35-64 2-31 (41)
74 KOG4215 Hepatocyte nuclear fac 23.9 62 0.0013 29.6 2.3 38 26-68 12-49 (432)
75 PF02701 zf-Dof: Dof domain, z 23.8 1.4E+02 0.0031 20.5 3.6 40 31-70 3-45 (63)
76 PF08274 PhnA_Zn_Ribbon: PhnA 23.4 24 0.00051 20.7 -0.2 25 34-63 3-27 (30)
77 PF10083 DUF2321: Uncharacteri 22.4 36 0.00078 27.3 0.5 33 34-66 40-79 (158)
78 PF13717 zinc_ribbon_4: zinc-r 22.4 19 0.0004 21.6 -0.9 29 35-63 4-33 (36)
79 PF09698 GSu_C4xC__C2xCH: Geob 22.2 50 0.0011 19.7 1.0 17 42-61 19-35 (36)
80 PHA00626 hypothetical protein 22.0 25 0.00055 23.8 -0.4 33 35-68 2-36 (59)
81 TIGR01384 TFS_arch transcripti 21.7 29 0.00063 24.6 -0.1 35 32-66 61-101 (104)
82 cd07169 NR_DBD_GCNF_like DNA-b 21.6 79 0.0017 22.4 2.1 34 31-69 4-37 (90)
83 PF05876 Terminase_GpA: Phage 21.3 39 0.00084 31.4 0.6 35 34-68 201-242 (557)
84 PRK00241 nudC NADH pyrophospha 20.5 41 0.00089 28.1 0.5 33 32-68 98-130 (256)
85 PRK00432 30S ribosomal protein 20.4 22 0.00047 22.9 -0.9 29 32-65 19-47 (50)
86 KOG1597 Transcription initiati 20.3 45 0.00098 29.4 0.7 32 35-67 2-33 (308)
87 PF12553 DUF3742: Protein of u 20.2 37 0.0008 22.4 0.2 10 45-54 34-43 (54)
88 KOG2691 RNA polymerase II subu 20.1 53 0.0012 25.0 1.0 41 26-66 66-112 (113)
89 cd07168 NR_DBD_DHR4_like DNA-b 20.1 95 0.0021 22.0 2.3 32 33-69 6-37 (90)
No 1
>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=99.58 E-value=3.7e-16 Score=95.35 Aligned_cols=35 Identities=54% Similarity=1.272 Sum_probs=28.3
Q ss_pred cccCCCCCCCccccCCCCCcccchhHHHHHHhhcc
Q 032112 36 CADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKRR 70 (147)
Q Consensus 36 C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~~ 70 (147)
|+||+|++||+||++|.|+.+|||+||+||+++++
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 89999999999999999987799999999998865
No 2
>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=99.58 E-value=8.7e-16 Score=101.47 Aligned_cols=38 Identities=53% Similarity=1.142 Sum_probs=34.6
Q ss_pred ccccCCCCCCCccccCCCCCcccchhHHHHHHhhcccc
Q 032112 35 TCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKRRAI 72 (147)
Q Consensus 35 ~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~~~~ 72 (147)
.|+||++++||+||+||.|..+|||||||||++++..+
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~r 38 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMR 38 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCCCC
Confidence 59999999999999999887899999999999887544
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.57 E-value=1.3e-15 Score=99.71 Aligned_cols=40 Identities=53% Similarity=1.168 Sum_probs=36.9
Q ss_pred CCCccccCCCCCCCccccCCCCCcccchhHHHHHHhhccc
Q 032112 32 IKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKRRA 71 (147)
Q Consensus 32 ~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~~~ 71 (147)
..+.|+||++++||+||++|.|+.+|||||||||++++..
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 4678999999999999999999889999999999998764
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.87 E-value=7.2e-10 Score=85.93 Aligned_cols=37 Identities=68% Similarity=1.409 Sum_probs=35.1
Q ss_pred CCccccCCCCCCCccccCCCCCcccchhHHHHHHhhc
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKR 69 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~ 69 (147)
...|++|+++.||+||+++.|++.+|||||++++++.
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~ 235 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGG 235 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcC
Confidence 5899999999999999999998899999999999886
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.71 E-value=4.3e-09 Score=95.48 Aligned_cols=56 Identities=36% Similarity=0.776 Sum_probs=42.5
Q ss_pred CCCCCCCCccccCCCCCCCccccCCC-----CCcccchhHHHHHHhhcccc--cccCchhhhhc
Q 032112 27 SDENSIKKTCADCGTTKTPLWRGGPA-----GPKSLCNACGIRSRKKRRAI--LGITKEEKKSK 83 (147)
Q Consensus 27 ~~~~~~~~~C~nCgtt~Tp~WR~gp~-----G~~~LCNaCGl~~~k~~~~~--~~~~~~~~k~k 83 (147)
+........|.||.|+.||+|||++. |. +||||||||++-++..+ ..++...++++
T Consensus 152 ~~~s~~~~vc~Nc~t~stPlwrR~~~~~s~~~n-~lcnaCgl~~klhg~~r~P~t~ks~~~ks~ 214 (498)
T COG5641 152 SDNSNQPHVCSNCKTTSTPLWRRASSESSLPGN-NLCNACGLYLKLHGSPRAPISLKSDSIKSR 214 (498)
T ss_pred cccccccchhccccccCCccccccccccccCCc-cccccccccccccCCcCCCccccccccccc
Confidence 33344455999999999999999999 64 99999999999888655 33444444443
No 6
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=95.83 E-value=0.0046 Score=56.73 Aligned_cols=92 Identities=22% Similarity=0.266 Sum_probs=63.2
Q ss_pred CCccccCCC-CCCCccccCCCCCcccchhHHHHHHhhcccccccCchhhhhc-----ccCCCCCC-----CCCCCCCCCc
Q 032112 33 KKTCADCGT-TKTPLWRGGPAGPKSLCNACGIRSRKKRRAILGITKEEKKSK-----RGNSNSSS-----NSSSNKLGDS 101 (147)
Q Consensus 33 ~~~C~nCgt-t~Tp~WR~gp~G~~~LCNaCGl~~~k~~~~~~~~~~~~~k~k-----~~~~~~~~-----~~~~~~~~~~ 101 (147)
...|.+|.+ +.||.||+...-.-++||+||++.+..+..+..+.+...-.+ +-++.... ........++
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d~n~~~~~~~~~N~s~~~~~k~~~~~~~~~s~~ 376 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPNSKRSNATCMNCSSTPTNKILSPPTTSNSPG 376 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCCcccccccCCCCChhhhhhhheecccccccccccccCcccccCcc
Confidence 567888887 789999888765569999999999988877765554433332 11221111 1122334578
Q ss_pred chhhhhccCcchhhhhhhHHHHh
Q 032112 102 LKQRLYALGREVLMQRSSVEKQR 124 (147)
Q Consensus 102 l~~kl~~v~r~~~mkk~~i~~rk 124 (147)
.+-+|++..+++.|++..|-+||
T Consensus 377 ~~~~l~N~t~~~~~~~~~~~~~r 399 (498)
T COG5641 377 AQVKLPNQTRSTGATKKKITRRR 399 (498)
T ss_pred chhhccCcccccccccccccccc
Confidence 89999999999999887765444
No 7
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=94.15 E-value=0.19 Score=46.74 Aligned_cols=39 Identities=31% Similarity=0.580 Sum_probs=31.8
Q ss_pred CCCCccccCCCCCCCccc-cCCCC-CcccchhHHHHHHhhc
Q 032112 31 SIKKTCADCGTTKTPLWR-GGPAG-PKSLCNACGIRSRKKR 69 (147)
Q Consensus 31 ~~~~~C~nCgtt~Tp~WR-~gp~G-~~~LCNaCGl~~~k~~ 69 (147)
..++.|-+|+|+++-+|= .||.+ ...||-.|=+||+|.+
T Consensus 384 ~~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKyg 424 (693)
T KOG3554|consen 384 QDGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYG 424 (693)
T ss_pred CCCCcccccccccccceeccCCCCccchhhHHHHHHHHHhc
Confidence 347899999999999993 45544 4579999999999876
No 8
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=84.10 E-value=0.29 Score=29.56 Aligned_cols=30 Identities=30% Similarity=0.674 Sum_probs=15.2
Q ss_pred CccccCCCCCCCccccCCCCCcccchhHHH
Q 032112 34 KTCADCGTTKTPLWRGGPAGPKSLCNACGI 63 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl 63 (147)
+.|.+||+.-+..-=.|.+-...+|.+||.
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 469999987433333556666789999983
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=81.38 E-value=1.3 Score=32.59 Aligned_cols=37 Identities=35% Similarity=0.646 Sum_probs=26.4
Q ss_pred CCCCccccCCCCCCCccccCCCCCcccchhHHHHHHhhc
Q 032112 31 SIKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKR 69 (147)
Q Consensus 31 ~~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~ 69 (147)
..++.|++|++.. |.|-.-..| ..||-.|.-.++..+
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 4568999999655 599999999 599999988888766
No 10
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=78.73 E-value=1 Score=39.33 Aligned_cols=39 Identities=36% Similarity=0.678 Sum_probs=32.7
Q ss_pred CCCCCccccCCCCCCCccccCCCCCcccchhHHHHHHhhcc
Q 032112 30 NSIKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKRR 70 (147)
Q Consensus 30 ~~~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~~ 70 (147)
...++.|++|+++. |.|-.-..| ..||-.|.=-+|.-+.
T Consensus 17 ~~~Nk~CaDCga~~-P~W~S~nlG-vfiCi~CagvHRsLGv 55 (319)
T COG5347 17 DSSNKKCADCGAPN-PTWASVNLG-VFLCIDCAGVHRSLGV 55 (319)
T ss_pred ccccCccccCCCCC-CceEecccC-eEEEeecchhhhcccc
Confidence 34578899999999 999999999 5999999777775553
No 11
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=75.54 E-value=0.81 Score=35.44 Aligned_cols=29 Identities=34% Similarity=0.753 Sum_probs=23.0
Q ss_pred CccccCCCCCCCccccCCCCCcccchhHHH
Q 032112 34 KTCADCGTTKTPLWRGGPAGPKSLCNACGI 63 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl 63 (147)
-.|..|+..+|-+=+.+..- -..|+|||-
T Consensus 103 VlC~~C~spdT~l~k~~r~~-~l~C~ACGa 131 (138)
T PRK03988 103 VICPECGSPDTKLIKEGRIW-VLKCEACGA 131 (138)
T ss_pred EECCCCCCCCcEEEEcCCeE-EEEcccCCC
Confidence 36999999999998764433 368999994
No 12
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=74.11 E-value=0.94 Score=34.90 Aligned_cols=30 Identities=27% Similarity=0.698 Sum_probs=23.0
Q ss_pred CccccCCCCCCCccccCCCCCcccchhHHHH
Q 032112 34 KTCADCGTTKTPLWRGGPAGPKSLCNACGIR 64 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~ 64 (147)
-.|..|+..+|-+-+.+..- -.-|+|||-.
T Consensus 98 VlC~~C~sPdT~l~k~~r~~-~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVS-LLKCEACGAK 127 (133)
T ss_pred EECCCCCCCCcEEEEeCCeE-EEecccCCCC
Confidence 46999999999998864332 2589999943
No 13
>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=73.97 E-value=3 Score=30.58 Aligned_cols=36 Identities=33% Similarity=0.633 Sum_probs=30.7
Q ss_pred CCCccccCCCCCCCccccCCCCCcccchhHHHHHHhhc
Q 032112 32 IKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKR 69 (147)
Q Consensus 32 ~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~ 69 (147)
.++.|++|+. .-|.|=.-..| ..||-.|.-.++..+
T Consensus 2 ~N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~lg 37 (112)
T smart00105 2 GNKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRSLG 37 (112)
T ss_pred CCCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHhcC
Confidence 4678999998 45999999999 499999988888765
No 14
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=73.68 E-value=1 Score=33.65 Aligned_cols=29 Identities=31% Similarity=0.638 Sum_probs=22.6
Q ss_pred CccccCCCCCCCccccCCCCCcccchhHHH
Q 032112 34 KTCADCGTTKTPLWRGGPAGPKSLCNACGI 63 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl 63 (147)
-.|..|+..+|-+=+.+..- -.-|+|||-
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 46999999999999874333 256999983
No 15
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=68.90 E-value=1.4 Score=35.75 Aligned_cols=32 Identities=28% Similarity=0.598 Sum_probs=24.4
Q ss_pred CccccCCCCCCCccccCCCCCcccchhHHHHHH
Q 032112 34 KTCADCGTTKTPLWRGGPAGPKSLCNACGIRSR 66 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~ 66 (147)
-.|..|+..+|-+-+.+..- ..-|+|||-..-
T Consensus 99 V~C~~C~~pdT~l~k~~~~~-~l~C~aCGa~~~ 130 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVL-MLRCDACGAHRP 130 (201)
T ss_pred EECCCCCCCCcEEEEcCCeE-EEEcccCCCCcc
Confidence 46999999999998765333 358999996543
No 16
>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=68.25 E-value=1.1 Score=29.28 Aligned_cols=27 Identities=7% Similarity=0.162 Sum_probs=21.8
Q ss_pred CCcchhhhhccCcchhhhh-hhHHHHhh
Q 032112 99 GDSLKQRLYALGREVLMQR-SSVEKQRK 125 (147)
Q Consensus 99 ~~~l~~kl~~v~r~~~mkk-~~i~~rkr 125 (147)
.||||++.++..||+.+.. +.|+++++
T Consensus 26 aCgl~~~k~~~~rp~~~~~~~~~~~~~~ 53 (54)
T cd00202 26 ACGLYWKKHGVMRPLSKRKKDQIKRRNR 53 (54)
T ss_pred HHHHHHHhcCCCCCcccCcccccccccC
Confidence 4899999999999999976 66655543
No 17
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=65.92 E-value=1.9 Score=28.67 Aligned_cols=24 Identities=33% Similarity=0.934 Sum_probs=18.9
Q ss_pred CCccccCCCCCCCccccCCCCCcccchhHHHHH
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLCNACGIRS 65 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~ 65 (147)
.-.|.+||...-| +.+|..||.|.
T Consensus 27 l~~C~~CG~~~~~---------H~vC~~CG~Y~ 50 (57)
T PRK12286 27 LVECPNCGEPKLP---------HRVCPSCGYYK 50 (57)
T ss_pred ceECCCCCCccCC---------eEECCCCCcCC
Confidence 3569999987766 68999999654
No 18
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=65.29 E-value=2.2 Score=26.17 Aligned_cols=28 Identities=25% Similarity=0.810 Sum_probs=17.5
Q ss_pred ccccCCCCCCCccccCCCCCcccchhHHHHH
Q 032112 35 TCADCGTTKTPLWRGGPAGPKSLCNACGIRS 65 (147)
Q Consensus 35 ~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~ 65 (147)
.|.+|+++. ..+ ....|. .+|..||+-.
T Consensus 2 ~Cp~Cg~~~-~~~-D~~~g~-~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKE-IVF-DPERGE-LVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSE-EEE-ETTTTE-EEETTT-BBE
T ss_pred CCcCCcCCc-eEE-cCCCCe-EECCCCCCEe
Confidence 588898876 233 344553 7899998643
No 19
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=65.04 E-value=4.5 Score=36.44 Aligned_cols=38 Identities=32% Similarity=0.586 Sum_probs=31.5
Q ss_pred CCCCccccCCCCCCCccccCCCCCcccchhHHHHHHhhcc
Q 032112 31 SIKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKRR 70 (147)
Q Consensus 31 ~~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~~ 70 (147)
..++.|.+|+... |.|-.-..| ..||..|.=.+|..+.
T Consensus 20 PgNk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRsLGv 57 (395)
T PLN03114 20 SDNKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRSLGV 57 (395)
T ss_pred cCCCcCccCCCCC-CCceeeccc-eeehhhhhHhhccCCC
Confidence 4578899999875 999999999 5999999877776553
No 20
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=64.06 E-value=3.3 Score=37.94 Aligned_cols=42 Identities=33% Similarity=0.610 Sum_probs=34.4
Q ss_pred CCCCCccccCCCCCCCccccCCCCCcccchhHHHHHHhhccccc
Q 032112 30 NSIKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKRRAIL 73 (147)
Q Consensus 30 ~~~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~~~~~ 73 (147)
...++.|++|+.. -|-|-.-+.| ..||-.|---+|--++...
T Consensus 20 ~~~NKvCFDCgAk-nPtWaSVTYG-IFLCiDCSAvHRnLGVHiS 61 (454)
T KOG0706|consen 20 QSENKVCFDCGAK-NPTWASVTYG-IFLCIDCSAVHRNLGVHIS 61 (454)
T ss_pred CCCCceecccCCC-CCCceeecce-EEEEEecchhhhccccceE
Confidence 4568999999986 5999999999 6999999888776666443
No 21
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=63.07 E-value=4.1 Score=39.00 Aligned_cols=40 Identities=23% Similarity=0.539 Sum_probs=31.3
Q ss_pred CCCCCCCCccccCCCCCCCccccCCCC---CcccchhHHHHHH
Q 032112 27 SDENSIKKTCADCGTTKTPLWRGGPAG---PKSLCNACGIRSR 66 (147)
Q Consensus 27 ~~~~~~~~~C~nCgtt~Tp~WR~gp~G---~~~LCNaCGl~~~ 66 (147)
.....++-.|..|.|.-||.|+.-+.+ .+++|.+|---..
T Consensus 456 t~~a~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSnq 498 (706)
T KOG3740|consen 456 TTLATEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSNQ 498 (706)
T ss_pred ccccCCchhhhhcccccccccccccccCcchHHHHHhhhhhcc
Confidence 345566778999999999999987776 3589999964433
No 22
>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=62.90 E-value=2.2 Score=32.50 Aligned_cols=29 Identities=34% Similarity=0.716 Sum_probs=23.5
Q ss_pred CccccCCCCCCCccccCCCCCcccchhHHH
Q 032112 34 KTCADCGTTKTPLWRGGPAGPKSLCNACGI 63 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl 63 (147)
-.|..|+..+|-+=..+..- ..-|+|||-
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 36999999999998885554 368999983
No 23
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=59.17 E-value=7.4 Score=34.34 Aligned_cols=30 Identities=30% Similarity=0.716 Sum_probs=22.6
Q ss_pred CCCCccccCCCCCCCccccCCCCCcccchhHHH
Q 032112 31 SIKKTCADCGTTKTPLWRGGPAGPKSLCNACGI 63 (147)
Q Consensus 31 ~~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl 63 (147)
.....|.|||.+.|+-.-+|.. -.|-+||-
T Consensus 313 ~k~nfc~ncG~~~t~~~~ng~a---~fcp~cgq 342 (345)
T COG4260 313 AKLNFCLNCGCGTTADFDNGKA---KFCPECGQ 342 (345)
T ss_pred cccccccccCcccccCCccchh---hhChhhcC
Confidence 4556999999998886655444 48999984
No 24
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=57.02 E-value=2.3 Score=29.28 Aligned_cols=34 Identities=21% Similarity=0.335 Sum_probs=26.8
Q ss_pred CCccccCCCCCCCccccCCCCCcccchhHHHHHH
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSR 66 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~ 66 (147)
...|..|.+..|-.|.+-..-+..-|-+||...+
T Consensus 10 GA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~ 43 (66)
T COG3529 10 GAVCPACQAQDTLAMWRENNVEIVECVKCGHHMR 43 (66)
T ss_pred cCCCcccchhhHHHHHHhcCCceEehhhcchHhh
Confidence 4579999999997765555555689999998765
No 25
>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=56.15 E-value=6.8 Score=24.04 Aligned_cols=29 Identities=24% Similarity=0.718 Sum_probs=21.8
Q ss_pred CCccccCCCCCCCccccC-CCCCcccchhHH
Q 032112 33 KKTCADCGTTKTPLWRGG-PAGPKSLCNACG 62 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~g-p~G~~~LCNaCG 62 (147)
...|..|+.+..-.|.+. ..| ..+|+.||
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 346999999988778653 345 47999996
No 26
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=53.57 E-value=5.3 Score=34.68 Aligned_cols=35 Identities=34% Similarity=0.695 Sum_probs=28.7
Q ss_pred CCccccCCCCCCCccccCCCCCcccchhHHHHHHhhc
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKR 69 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~ 69 (147)
++.|++|++. .|.|-.--.| ..+|-.|-=-+|.-+
T Consensus 25 N~~CADC~a~-~P~WaSwnlG-vFiC~~C~giHR~lg 59 (287)
T KOG0703|consen 25 NKVCADCGAK-GPRWASWNLG-VFICLRCAGIHRSLG 59 (287)
T ss_pred cCcccccCCC-CCCeEEeecC-eEEEeeccccccccc
Confidence 7899999999 9999998899 599999954444433
No 27
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=53.57 E-value=13 Score=25.40 Aligned_cols=36 Identities=31% Similarity=0.572 Sum_probs=25.4
Q ss_pred CCCCCCCccccCCCCCCCccccCCCCCcccchhHHHHHHhh
Q 032112 28 DENSIKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKK 68 (147)
Q Consensus 28 ~~~~~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~ 68 (147)
......-.|..|++-.|-.- +...-|-.||.+.-.+
T Consensus 15 r~~~miYiCgdC~~en~lk~-----~D~irCReCG~RIlyK 50 (62)
T KOG3507|consen 15 RTATMIYICGDCGQENTLKR-----GDVIRCRECGYRILYK 50 (62)
T ss_pred CcccEEEEeccccccccccC-----CCcEehhhcchHHHHH
Confidence 44556679999999887542 3357899999765443
No 28
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=53.20 E-value=4 Score=30.06 Aligned_cols=36 Identities=17% Similarity=0.313 Sum_probs=22.8
Q ss_pred CCccccCCCCCCCccccCCCCCcccchhHHHHHHhhc
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKR 69 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~ 69 (147)
.-.|.+|+.. +..-..+-...+..|..||.|+-..-
T Consensus 21 ~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y~~~~V 56 (99)
T PRK14892 21 IFECPRCGKV-SISVKIKKNIAIITCGNCGLYTEFEV 56 (99)
T ss_pred EeECCCCCCe-EeeeecCCCcceEECCCCCCccCEEC
Confidence 4579999953 22211122344789999999977643
No 29
>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=51.15 E-value=3.6 Score=26.96 Aligned_cols=22 Identities=36% Similarity=1.016 Sum_probs=16.2
Q ss_pred CCCccccCCCCCCCccccCCCCCcccchhHH
Q 032112 32 IKKTCADCGTTKTPLWRGGPAGPKSLCNACG 62 (147)
Q Consensus 32 ~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCG 62 (147)
..-.|.+||...- ++.+|..||
T Consensus 25 ~l~~c~~cg~~~~---------~H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKL---------PHRVCPSCG 46 (56)
T ss_dssp SEEESSSSSSEES---------TTSBCTTTB
T ss_pred ceeeeccCCCEec---------ccEeeCCCC
Confidence 3467999986433 368999999
No 30
>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=49.47 E-value=7 Score=24.45 Aligned_cols=24 Identities=50% Similarity=1.128 Sum_probs=18.1
Q ss_pred CccccCCCCCCCccccCCCCCcccchhHH
Q 032112 34 KTCADCGTTKTPLWRGGPAGPKSLCNACG 62 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~gp~G~~~LCNaCG 62 (147)
..|..| .||+.| ...| ..+|-+|+
T Consensus 18 ~~Cp~C---~~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDC---GTPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred CccCCC---CCeeEE-ecCC-CEECCCCC
Confidence 468888 489999 4456 47999885
No 31
>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=48.82 E-value=8.3 Score=23.75 Aligned_cols=31 Identities=32% Similarity=0.828 Sum_probs=18.8
Q ss_pred CccccCCCCCCCccc--cCCCCCcccchhHHHHH
Q 032112 34 KTCADCGTTKTPLWR--GGPAGPKSLCNACGIRS 65 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR--~gp~G~~~LCNaCGl~~ 65 (147)
+.|+-||.+.+..=+ .|+.+ ..+|+.|-...
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 579999999864422 67766 48999997653
No 32
>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=47.75 E-value=5.3 Score=27.70 Aligned_cols=35 Identities=20% Similarity=0.410 Sum_probs=27.5
Q ss_pred CCccccCCCCCCCccccCCCCCcccchhHHHHHHh
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRK 67 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k 67 (147)
+-.|..|++..|-.|.........-|-+||..-..
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~ 42 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQ 42 (71)
T ss_pred CccCCCCcCccEEEEEEeCCceEEEecCCCCeecc
Confidence 45799999999988765555667899999977653
No 33
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=47.10 E-value=8.2 Score=32.97 Aligned_cols=30 Identities=30% Similarity=0.712 Sum_probs=17.6
Q ss_pred CCccccCCCCCCCccccCCCCCcccchhHHHHH
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLCNACGIRS 65 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~ 65 (147)
...|.+|+. ++.--+-..|. .+|..||+-.
T Consensus 11 ~~~Cp~Cg~--~~iv~d~~~Ge-~vC~~CG~Vl 40 (310)
T PRK00423 11 KLVCPECGS--DKLIYDYERGE-IVCADCGLVI 40 (310)
T ss_pred CCcCcCCCC--CCeeEECCCCe-EeecccCCcc
Confidence 346777875 23333345664 7788887643
No 34
>COG3952 Predicted membrane protein [Function unknown]
Probab=46.02 E-value=5.2 Score=30.32 Aligned_cols=19 Identities=32% Similarity=0.452 Sum_probs=14.3
Q ss_pred ccccCCCCCcccchhHHHHHH
Q 032112 46 LWRGGPAGPKSLCNACGIRSR 66 (147)
Q Consensus 46 ~WR~gp~G~~~LCNaCGl~~~ 66 (147)
+||.+|-+ .+|++||++--
T Consensus 76 i~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HHhcchHH--HHHHhhhHHHH
Confidence 36677777 79999998743
No 35
>PF12773 DZR: Double zinc ribbon
Probab=45.63 E-value=14 Score=22.76 Aligned_cols=29 Identities=34% Similarity=0.775 Sum_probs=16.0
Q ss_pred CCCCccccCCCCCCCccccCCCCCcccchhHHHH
Q 032112 31 SIKKTCADCGTTKTPLWRGGPAGPKSLCNACGIR 64 (147)
Q Consensus 31 ~~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~ 64 (147)
...+.|.+||+.-. .+......|..||-.
T Consensus 10 ~~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 10 DDAKFCPHCGTPLP-----PPDQSKKICPNCGAE 38 (50)
T ss_pred ccccCChhhcCChh-----hccCCCCCCcCCcCC
Confidence 33566777777665 222223566666643
No 36
>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=45.50 E-value=12 Score=24.60 Aligned_cols=30 Identities=27% Similarity=0.671 Sum_probs=21.2
Q ss_pred CCCccccCCCCCCCccccCCCCCcccchhHHHHH
Q 032112 32 IKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRS 65 (147)
Q Consensus 32 ~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~ 65 (147)
....|+.||..... ...+....|..||..+
T Consensus 27 TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK----RRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCccCccccccc----ccccceEEcCCCCCEE
Confidence 45569999987655 3344457999999764
No 37
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=45.31 E-value=2.1 Score=26.13 Aligned_cols=31 Identities=26% Similarity=0.651 Sum_probs=18.9
Q ss_pred ccccCCCCCCCcc----ccCCCCC--cccchhHHHHH
Q 032112 35 TCADCGTTKTPLW----RGGPAGP--KSLCNACGIRS 65 (147)
Q Consensus 35 ~C~nCgtt~Tp~W----R~gp~G~--~~LCNaCGl~~ 65 (147)
.|.+|+-.++-.| |.++++. -+.|..||-.|
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 5888998876555 5555553 25788888655
No 38
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core
Probab=44.07 E-value=41 Score=24.87 Aligned_cols=33 Identities=21% Similarity=0.475 Sum_probs=22.9
Q ss_pred CCCccccCCCCCCCccccCCCCCcccchhHHHHHHhhc
Q 032112 32 IKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKR 69 (147)
Q Consensus 32 ~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~ 69 (147)
....|..|+...+-.+ .| ...|+||..+++..-
T Consensus 5 ~~~~C~VCg~~a~g~h----yG-v~sC~aCk~FFRR~v 37 (107)
T cd06955 5 VPRICGVCGDRATGFH----FN-AMTCEGCKGFFRRSM 37 (107)
T ss_pred CCCCCeecCCcCcccE----EC-cceeeeecceeccee
Confidence 3456999997555332 23 368999999998654
No 39
>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=43.71 E-value=6.6 Score=25.86 Aligned_cols=23 Identities=35% Similarity=0.941 Sum_probs=16.8
Q ss_pred CCccccCCCCCCCccccCCCCCcccchhHHHH
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLCNACGIR 64 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~ 64 (147)
.-.|.+||...-| +.+|-.||.|
T Consensus 26 l~~C~~cG~~~~~---------H~vc~~cG~Y 48 (55)
T TIGR01031 26 LVVCPNCGEFKLP---------HRVCPSCGYY 48 (55)
T ss_pred ceECCCCCCcccC---------eeECCccCeE
Confidence 3469999875543 6899999944
No 40
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=42.37 E-value=8.3 Score=25.84 Aligned_cols=24 Identities=13% Similarity=0.102 Sum_probs=17.4
Q ss_pred CCccccCCCCCCCccccCCCCCcccchhHHHHHH
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSR 66 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~ 66 (147)
.-.|.+||+..-| +.+|. ||.|.-
T Consensus 27 ~~~c~~cg~~~~p---------H~vc~-cG~Y~g 50 (60)
T PRK01110 27 LSVDKTTGEYHLP---------HHVSP-KGYYKG 50 (60)
T ss_pred eeEcCCCCceecc---------ceecC-CcccCC
Confidence 4578899887655 57899 996643
No 41
>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=40.83 E-value=13 Score=23.06 Aligned_cols=26 Identities=31% Similarity=0.690 Sum_probs=18.5
Q ss_pred CccccCCCCCCCccccCCCCCcccchhHH
Q 032112 34 KTCADCGTTKTPLWRGGPAGPKSLCNACG 62 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~gp~G~~~LCNaCG 62 (147)
..|.+||.+ ..-|-++ .+ ..-|++|+
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 5555544 33 47899886
No 42
>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=40.14 E-value=9.1 Score=23.50 Aligned_cols=28 Identities=25% Similarity=0.541 Sum_probs=17.5
Q ss_pred ccccCCCCCCCccccCCCCCcccchhHHH
Q 032112 35 TCADCGTTKTPLWRGGPAGPKSLCNACGI 63 (147)
Q Consensus 35 ~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl 63 (147)
.|..||..-+-+..-.. .....|-.||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 57788876655544444 33467888875
No 43
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=40.02 E-value=15 Score=35.14 Aligned_cols=36 Identities=19% Similarity=0.390 Sum_probs=29.0
Q ss_pred CCCCccccCCCCCCCccccCCCCCcccchhHHHHHHhh
Q 032112 31 SIKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKK 68 (147)
Q Consensus 31 ~~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~ 68 (147)
..++.|++|+... |.|-.-..| ..+|-.|.=.+|..
T Consensus 21 PgNk~CADCgs~~-P~WASiNlG-IFICi~CSGIHRsL 56 (648)
T PLN03119 21 PPNRRCINCNSLG-PQYVCTTFW-TFVCMACSGIHREF 56 (648)
T ss_pred cCCCccccCCCCC-CCceeeccc-eEEeccchhhhccC
Confidence 4568999999876 999999999 48999996555543
No 44
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=39.93 E-value=18 Score=24.56 Aligned_cols=15 Identities=27% Similarity=0.838 Sum_probs=13.2
Q ss_pred ccccCCCCC-CCcccc
Q 032112 35 TCADCGTTK-TPLWRG 49 (147)
Q Consensus 35 ~C~nCgtt~-Tp~WR~ 49 (147)
.|.+|+++. |..|..
T Consensus 17 ~CP~Cgs~~~T~~W~G 32 (61)
T PRK08351 17 RCPVCGSRDLSDEWFD 32 (61)
T ss_pred cCCCCcCCcccccccc
Confidence 699999998 999985
No 45
>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=38.20 E-value=9.5 Score=25.90 Aligned_cols=34 Identities=18% Similarity=0.348 Sum_probs=25.6
Q ss_pred CCccccCCCCCCCccccCCCCCcccchhHHHHHH
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSR 66 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~ 66 (147)
+-.|..|++..|-.|-....-...-|-.||....
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~ 42 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNIELVECVECGYQEQ 42 (59)
T ss_pred cccCCCCcCccEEEEEEeCCceEEEeccCCCccc
Confidence 4579999999987765444444689999997654
No 46
>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=37.68 E-value=16 Score=22.09 Aligned_cols=27 Identities=30% Similarity=0.791 Sum_probs=20.0
Q ss_pred CCCccccCCCCCCCccccCCCCCcccchhHHH
Q 032112 32 IKKTCADCGTTKTPLWRGGPAGPKSLCNACGI 63 (147)
Q Consensus 32 ~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl 63 (147)
....|..|+.. |-...+|. ..|..||-
T Consensus 7 ~~~~C~~C~~~----~~~~~dG~-~yC~~cG~ 33 (36)
T PF11781_consen 7 PNEPCPVCGSR----WFYSDDGF-YYCDRCGH 33 (36)
T ss_pred CCCcCCCCCCe----EeEccCCE-EEhhhCce
Confidence 34459999987 66667774 89999984
No 47
>PRK00420 hypothetical protein; Validated
Probab=37.43 E-value=16 Score=27.56 Aligned_cols=29 Identities=31% Similarity=0.635 Sum_probs=21.7
Q ss_pred CCccccCCCCCCCccccCCCCCcccchhHHHHHH
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSR 66 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~ 66 (147)
...|..|| +|+.+- ..| ...|-.||-.+.
T Consensus 23 ~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCC---Ccceec-CCC-ceECCCCCCeee
Confidence 35688888 688875 455 479999997655
No 48
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=35.74 E-value=14 Score=23.26 Aligned_cols=30 Identities=27% Similarity=0.632 Sum_probs=21.1
Q ss_pred ccccCCCCCCCccccCCCCCcccchhHHHHHHhhc
Q 032112 35 TCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKR 69 (147)
Q Consensus 35 ~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~ 69 (147)
.|.+||...+.. +.+ ..-|..||-+.-.+.
T Consensus 4 ~C~~Cg~~~~~~----~~~-~irC~~CG~rIlyK~ 33 (44)
T smart00659 4 ICGECGRENEIK----SKD-VVRCRECGYRILYKK 33 (44)
T ss_pred ECCCCCCEeecC----CCC-ceECCCCCceEEEEe
Confidence 699999987755 223 378999997755443
No 49
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=34.42 E-value=25 Score=24.16 Aligned_cols=16 Identities=44% Similarity=0.729 Sum_probs=12.9
Q ss_pred CCccccCCCCC-CCccc
Q 032112 33 KKTCADCGTTK-TPLWR 48 (147)
Q Consensus 33 ~~~C~nCgtt~-Tp~WR 48 (147)
...|.+||++. |+.|.
T Consensus 17 ~~~Cp~Cgs~~~S~~w~ 33 (64)
T PRK06393 17 EKTCPVHGDEKTTTEWF 33 (64)
T ss_pred CCcCCCCCCCcCCcCcc
Confidence 34799999988 78886
No 50
>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=34.08 E-value=16 Score=22.74 Aligned_cols=26 Identities=23% Similarity=0.627 Sum_probs=15.9
Q ss_pred ccccCCCCCCCc-cccC-CCCCcccchhH
Q 032112 35 TCADCGTTKTPL-WRGG-PAGPKSLCNAC 61 (147)
Q Consensus 35 ~C~nCgtt~Tp~-WR~g-p~G~~~LCNaC 61 (147)
.|..|+.+.--. |... ..| ..+|+.|
T Consensus 5 pCP~CGG~DrFri~~d~~~~G-~~~C~~C 32 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRG-TWICRQC 32 (40)
T ss_dssp --TTTT-TTTEEEETT----S--EEETTT
T ss_pred CCCCCcCccccccCcCcccCC-CEECCCC
Confidence 689999988777 8753 335 5899999
No 51
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=34.08 E-value=9.1 Score=22.73 Aligned_cols=26 Identities=31% Similarity=0.737 Sum_probs=15.4
Q ss_pred ccccCCCCCCCccccCCCCCcccchhHHHHH
Q 032112 35 TCADCGTTKTPLWRGGPAGPKSLCNACGIRS 65 (147)
Q Consensus 35 ~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~ 65 (147)
.|.+|++...-. .+...-|..||-+.
T Consensus 2 ~C~~Cg~~~~~~-----~~~~irC~~CG~RI 27 (32)
T PF03604_consen 2 ICGECGAEVELK-----PGDPIRCPECGHRI 27 (32)
T ss_dssp BESSSSSSE-BS-----TSSTSSBSSSS-SE
T ss_pred CCCcCCCeeEcC-----CCCcEECCcCCCeE
Confidence 488888877622 12236788888654
No 52
>PLN03131 hypothetical protein; Provisional
Probab=33.85 E-value=23 Score=34.15 Aligned_cols=35 Identities=17% Similarity=0.411 Sum_probs=28.3
Q ss_pred CCCCccccCCCCCCCccccCCCCCcccchhHHHHHHh
Q 032112 31 SIKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRK 67 (147)
Q Consensus 31 ~~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k 67 (147)
..++.|++|+... |.|-.-..| ..||-.|.=.+|.
T Consensus 21 PgNk~CADCga~~-P~WASiNlG-IFICi~CSGIHRs 55 (705)
T PLN03131 21 PPNRRCINCNSLG-PQFVCTNFW-TFICMTCSGIHRE 55 (705)
T ss_pred cCCCccccCCCCC-CCeeEeccc-eEEchhchhhhcc
Confidence 4568999999865 999999999 5899999655554
No 53
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=33.76 E-value=8.2 Score=23.63 Aligned_cols=32 Identities=28% Similarity=0.723 Sum_probs=21.4
Q ss_pred ccccCCCCCCCcc----ccCCCCC--cccchhHHHHHH
Q 032112 35 TCADCGTTKTPLW----RGGPAGP--KSLCNACGIRSR 66 (147)
Q Consensus 35 ~C~nCgtt~Tp~W----R~gp~G~--~~LCNaCGl~~~ 66 (147)
.|.+|+-.+.-.| |...++. -+.|-.||-.|+
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeC
Confidence 5888987775555 5555553 357888886664
No 54
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=33.35 E-value=64 Score=23.13 Aligned_cols=31 Identities=23% Similarity=0.456 Sum_probs=20.9
Q ss_pred CccccCCCCCCCccccCCCCCcccchhHHHHHHhhc
Q 032112 34 KTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKR 69 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~ 69 (147)
+.|..|+...+-.+ .| ...|+||..+++...
T Consensus 1 ~~C~VCg~~a~g~h----yG-v~sC~aC~~FFRR~v 31 (94)
T cd06966 1 KICGVCGDKALGYN----FN-AITCESCKAFFRRNA 31 (94)
T ss_pred CCCeeCCCcCcceE----EC-cceeeeehheehhcc
Confidence 35888886544332 23 367999999998654
No 55
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=33.04 E-value=16 Score=31.54 Aligned_cols=34 Identities=26% Similarity=0.597 Sum_probs=25.3
Q ss_pred CCCccccCCCCCCCccccCCCCCcccchhHHHHHHhhc
Q 032112 32 IKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKR 69 (147)
Q Consensus 32 ~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~ 69 (147)
..+-|..||+...|. ..|-..+|+.||..+...-
T Consensus 110 ~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~fPR~ 143 (279)
T COG2816 110 SHRFCGRCGTKTYPR----EGGWARVCPKCGHEHFPRI 143 (279)
T ss_pred hCcCCCCCCCcCccc----cCceeeeCCCCCCccCCCC
Confidence 458899999988763 2333579999999887543
No 56
>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=32.72 E-value=19 Score=21.84 Aligned_cols=31 Identities=26% Similarity=0.609 Sum_probs=19.0
Q ss_pred CCccccCCCCCCCccccCCCCCcccchhHHH
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLCNACGI 63 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl 63 (147)
..+|.+|++---|.-.=...|..-.||-|+.
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 4579999998888877666766679999985
No 57
>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=31.52 E-value=19 Score=30.29 Aligned_cols=15 Identities=60% Similarity=0.953 Sum_probs=13.6
Q ss_pred HHHHHHHHhhccccC
Q 032112 133 AAVLLMALSYGSVYA 147 (147)
Q Consensus 133 aA~llmalS~g~v~a 147 (147)
=|.||..+||||+||
T Consensus 120 lAsll~S~sy~Sa~A 134 (246)
T PF10897_consen 120 LASLLISFSYGSAYA 134 (246)
T ss_pred HHHHHHHHHHhHHHH
Confidence 589999999999986
No 58
>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=31.49 E-value=14 Score=31.98 Aligned_cols=36 Identities=25% Similarity=0.480 Sum_probs=25.6
Q ss_pred CCCCccccCCCCCCCcc----ccCCCCC--cccchhHHHHHH
Q 032112 31 SIKKTCADCGTTKTPLW----RGGPAGP--KSLCNACGIRSR 66 (147)
Q Consensus 31 ~~~~~C~nCgtt~Tp~W----R~gp~G~--~~LCNaCGl~~~ 66 (147)
.....|..|+-.++..| |...++- -+.|..||.+|+
T Consensus 256 t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 256 TDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 33578999998887766 3333332 258999999886
No 59
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=31.46 E-value=18 Score=22.47 Aligned_cols=28 Identities=25% Similarity=0.637 Sum_probs=17.8
Q ss_pred ccccCCCCCCCccccCCCCCcccchhHHH
Q 032112 35 TCADCGTTKTPLWRGGPAGPKSLCNACGI 63 (147)
Q Consensus 35 ~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl 63 (147)
.|.+|+..-+ .|+.-.+.....|-.||-
T Consensus 7 ~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFE-VLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeE-EEEecCCCCCCCCCCCCC
Confidence 5888887554 465433333467888886
No 60
>PF15396 FAM60A: Protein Family FAM60A
Probab=30.80 E-value=28 Score=29.13 Aligned_cols=15 Identities=27% Similarity=0.796 Sum_probs=12.1
Q ss_pred ccchhHHHHHHhhcc
Q 032112 56 SLCNACGIRSRKKRR 70 (147)
Q Consensus 56 ~LCNaCGl~~~k~~~ 70 (147)
.+||||-|..++-++
T Consensus 50 eICNACVLLVKRwKK 64 (213)
T PF15396_consen 50 EICNACVLLVKRWKK 64 (213)
T ss_pred hhhHHHHHHHHHHhh
Confidence 699999999876544
No 61
>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=30.25 E-value=7.3 Score=22.46 Aligned_cols=28 Identities=29% Similarity=0.720 Sum_probs=14.5
Q ss_pred CCccccCCCCCCCccccCCCCCcccchhHHHH
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLCNACGIR 64 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~ 64 (147)
.+.|..||+...+.. .|....|.+||..
T Consensus 3 ~rfC~~CG~~t~~~~----~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAP----GGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-S----SSS-EEESSSS-E
T ss_pred CcccCcCCccccCCC----CcCEeECCCCcCE
Confidence 467888988765432 2334688888864
No 62
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=29.98 E-value=29 Score=32.55 Aligned_cols=29 Identities=31% Similarity=0.701 Sum_probs=19.3
Q ss_pred CccccCCCCCCCccccCCCCCcccchhHHHHH
Q 032112 34 KTCADCGTTKTPLWRGGPAGPKSLCNACGIRS 65 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~ 65 (147)
+.|.||+.+.= =|+...|. ..|++||.-.
T Consensus 1 ~~C~~C~~s~f--e~d~a~g~-~~C~~CG~v~ 29 (521)
T KOG1598|consen 1 MVCKNCGGSNF--ERDEATGN-LYCTACGTVL 29 (521)
T ss_pred CcCCCCCCCCc--ccccccCC-ceecccccee
Confidence 36999998642 13335565 7899998543
No 63
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=28.37 E-value=27 Score=27.98 Aligned_cols=28 Identities=29% Similarity=0.757 Sum_probs=23.3
Q ss_pred CccccCCCCCCCccccCCCCCcccchhHH
Q 032112 34 KTCADCGTTKTPLWRGGPAGPKSLCNACG 62 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~gp~G~~~LCNaCG 62 (147)
..|..||+.....|-.-..| ..+|..|+
T Consensus 150 ~~C~~Cg~~~~~~~f~~~~g-g~~c~~c~ 177 (247)
T PRK00085 150 DHCAVCGAPGDHRYFSPKEG-GAVCSECG 177 (247)
T ss_pred hhHhcCCCCCCceEEecccC-Cccccccc
Confidence 47999999887777777777 58999997
No 64
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=27.92 E-value=33 Score=21.07 Aligned_cols=29 Identities=24% Similarity=0.665 Sum_probs=18.6
Q ss_pred ccccCCCCCCCc-cccCCCCCcccchhHHHHHH
Q 032112 35 TCADCGTTKTPL-WRGGPAGPKSLCNACGIRSR 66 (147)
Q Consensus 35 ~C~nCgtt~Tp~-WR~gp~G~~~LCNaCGl~~~ 66 (147)
.|..||..-.+. |. ......|..||..+.
T Consensus 2 FCp~Cg~~l~~~~~~---~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNMLIPKEGK---EKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCccccccCC---CCCEEECCcCCCeEE
Confidence 588998855443 22 123578999995544
No 65
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=27.58 E-value=25 Score=32.59 Aligned_cols=34 Identities=29% Similarity=0.640 Sum_probs=22.6
Q ss_pred CCccccCCCCC-CCccccCCCCC----------cccchhHHHHHH
Q 032112 33 KKTCADCGTTK-TPLWRGGPAGP----------KSLCNACGIRSR 66 (147)
Q Consensus 33 ~~~C~nCgtt~-Tp~WR~gp~G~----------~~LCNaCGl~~~ 66 (147)
.+.|.+||.-. +++=+-+|.+. .+.||+||.--+
T Consensus 161 ~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~R 205 (500)
T KOG0909|consen 161 NPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETR 205 (500)
T ss_pred CCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCccc
Confidence 56799999877 44444333321 378999997655
No 66
>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=26.62 E-value=22 Score=20.77 Aligned_cols=28 Identities=32% Similarity=0.710 Sum_probs=16.7
Q ss_pred ccccCCCCCCCccccCCCCCcccchhHHH
Q 032112 35 TCADCGTTKTPLWRGGPAGPKSLCNACGI 63 (147)
Q Consensus 35 ~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl 63 (147)
.|..||..-+ .|.....+....|-.||-
T Consensus 7 ~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFE-VLQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEE-EEEecCCCCCCCCCCCCC
Confidence 5788887544 233322244467888886
No 67
>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=26.57 E-value=46 Score=22.35 Aligned_cols=30 Identities=33% Similarity=0.812 Sum_probs=22.8
Q ss_pred CCccccCCCCCCCccccCCCCCcccc-hhHHHHHHhhcc
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLC-NACGIRSRKKRR 70 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LC-NaCGl~~~k~~~ 70 (147)
-+-|.+||...-| . ...| ..|+--|.++.+
T Consensus 3 HkHC~~CG~~Ip~-------~-~~fCS~~C~~~~~k~qk 33 (59)
T PF09889_consen 3 HKHCPVCGKPIPP-------D-ESFCSPKCREEYRKRQK 33 (59)
T ss_pred CCcCCcCCCcCCc-------c-hhhhCHHHHHHHHHHHH
Confidence 3679999987654 2 4799 599999887665
No 68
>PHA02998 RNA polymerase subunit; Provisional
Probab=26.38 E-value=20 Score=29.60 Aligned_cols=36 Identities=19% Similarity=0.541 Sum_probs=28.1
Q ss_pred CCCccccCCCCCCCcc----ccCCCCC--cccchhHHHHHHh
Q 032112 32 IKKTCADCGTTKTPLW----RGGPAGP--KSLCNACGIRSRK 67 (147)
Q Consensus 32 ~~~~C~nCgtt~Tp~W----R~gp~G~--~~LCNaCGl~~~k 67 (147)
....|..|+-.++--| |.+.++. -+.|..||-.|+.
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 4567999999988776 6676664 2489999999984
No 69
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=26.15 E-value=1.5e+02 Score=20.78 Aligned_cols=30 Identities=23% Similarity=0.421 Sum_probs=19.9
Q ss_pred ccccCCCCCCCccccCCCCCcccchhHHHHHHhhc
Q 032112 35 TCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKR 69 (147)
Q Consensus 35 ~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~ 69 (147)
.|.-|+...+-. -.| ...|+||..+++..-
T Consensus 1 ~C~VCg~~~~g~----hyg-v~sC~aC~~FFRR~v 30 (87)
T cd07162 1 ICRVCGDRATGY----HFN-AMTCEGCKGFFRRAM 30 (87)
T ss_pred CCcccCCcCcce----EEC-cceehhhHHHHHhhh
Confidence 377787644432 134 368999999998754
No 70
>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=25.48 E-value=29 Score=28.01 Aligned_cols=29 Identities=31% Similarity=0.773 Sum_probs=23.3
Q ss_pred ccccCCCCCCCccccCCCCC--cccchhHHH
Q 032112 35 TCADCGTTKTPLWRGGPAGP--KSLCNACGI 63 (147)
Q Consensus 35 ~C~nCgtt~Tp~WR~gp~G~--~~LCNaCGl 63 (147)
.|.+||..-..+++.-..|. -+.|..||-
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~ 32 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCGK 32 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccCC
Confidence 69999999999998865553 368999973
No 71
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=25.31 E-value=25 Score=30.25 Aligned_cols=29 Identities=28% Similarity=0.772 Sum_probs=15.9
Q ss_pred ccccCCCCCCCccccCCCCCcccchhHHHHHH
Q 032112 35 TCADCGTTKTPLWRGGPAGPKSLCNACGIRSR 66 (147)
Q Consensus 35 ~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~ 66 (147)
.|.+|+.+ -.=..-..|. .+|-.||+-..
T Consensus 3 ~CpeCg~~--~~~~d~~~ge-~VC~~CG~Vi~ 31 (285)
T COG1405 3 SCPECGST--NIITDYERGE-IVCADCGLVLE 31 (285)
T ss_pred CCCCCCCc--cceeeccCCe-EEeccCCEEec
Confidence 47777776 2222223453 67777775433
No 72
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=24.73 E-value=23 Score=27.93 Aligned_cols=31 Identities=29% Similarity=0.573 Sum_probs=24.8
Q ss_pred CccccCCCCCCCccccCCCCCcccchhHHHHH
Q 032112 34 KTCADCGTTKTPLWRGGPAGPKSLCNACGIRS 65 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~ 65 (147)
..|.-|+...|++-+.+..- ...|-|||-..
T Consensus 106 v~C~~c~s~dt~l~~~~R~~-~l~c~acGa~~ 136 (151)
T COG1601 106 VKCKECGSPDTELIKEERLL-FLKCEACGAIR 136 (151)
T ss_pred eEeccCCCCchhhhhhhhhH-hhHHHHhCCcc
Confidence 57999999999999885544 36899999543
No 73
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=24.02 E-value=54 Score=20.15 Aligned_cols=30 Identities=23% Similarity=0.527 Sum_probs=21.1
Q ss_pred ccccCCCCCCCccccCCCCCcccchhHHHH
Q 032112 35 TCADCGTTKTPLWRGGPAGPKSLCNACGIR 64 (147)
Q Consensus 35 ~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~ 64 (147)
.|..|....++.|+=..-..-.||..|-..
T Consensus 2 ~C~~C~~~~~~r~~C~~C~dfDLC~~C~~~ 31 (41)
T cd02337 2 TCNECKHHVETRWHCTVCEDYDLCITCYNT 31 (41)
T ss_pred cCCCCCCcCCCceECCCCcchhhHHHHhCC
Confidence 377787766788876655555689988543
No 74
>KOG4215 consensus Hepatocyte nuclear factor 4 and similar steroid hormone receptors [Transcription]
Probab=23.89 E-value=62 Score=29.59 Aligned_cols=38 Identities=24% Similarity=0.447 Sum_probs=26.7
Q ss_pred CCCCCCCCCccccCCCCCCCccccCCCCCcccchhHHHHHHhh
Q 032112 26 SSDENSIKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKK 68 (147)
Q Consensus 26 ~~~~~~~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~ 68 (147)
+.+.+...-.|+-||...|- .-.|. +-||.|-=++|+-
T Consensus 12 ~~~~s~~~~~CaICGDkaTG----KHYGA-~SCdGCKGFFRRS 49 (432)
T KOG4215|consen 12 LQSSSGVAEFCAICGDKATG----KHYGA-ISCDGCKGFFRRS 49 (432)
T ss_pred cCCcccccchhheeCCcccc----cccce-eecCcchHHHHHH
Confidence 34556678899999988772 33564 7999995555543
No 75
>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=23.76 E-value=1.4e+02 Score=20.52 Aligned_cols=40 Identities=18% Similarity=0.463 Sum_probs=29.6
Q ss_pred CCCCccccCCCCCCCc--ccc-CCCCCcccchhHHHHHHhhcc
Q 032112 31 SIKKTCADCGTTKTPL--WRG-GPAGPKSLCNACGIRSRKKRR 70 (147)
Q Consensus 31 ~~~~~C~nCgtt~Tp~--WR~-gp~G~~~LCNaCGl~~~k~~~ 70 (147)
.+...|..|..+.|-- .-+ ...-|.+.|-+|-.||-..+.
T Consensus 3 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~ 45 (63)
T PF02701_consen 3 EQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGT 45 (63)
T ss_pred ccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcce
Confidence 3567899999998865 233 233557899999999998764
No 76
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=23.42 E-value=24 Score=20.72 Aligned_cols=25 Identities=32% Similarity=0.713 Sum_probs=12.4
Q ss_pred CccccCCCCCCCccccCCCCCcccchhHHH
Q 032112 34 KTCADCGTTKTPLWRGGPAGPKSLCNACGI 63 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl 63 (147)
..|-.|+...|= .+|..++|..||-
T Consensus 3 p~Cp~C~se~~y-----~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 3 PKCPLCGSEYTY-----EDGELLVCPECGH 27 (30)
T ss_dssp ---TTT-----E-----E-SSSEEETTTTE
T ss_pred CCCCCCCCccee-----ccCCEEeCCcccc
Confidence 358888888775 6666789998874
No 77
>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=22.42 E-value=36 Score=27.29 Aligned_cols=33 Identities=24% Similarity=0.533 Sum_probs=20.2
Q ss_pred CccccCCCCCCCcccc-------CCCCCcccchhHHHHHH
Q 032112 34 KTCADCGTTKTPLWRG-------GPAGPKSLCNACGIRSR 66 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~-------gp~G~~~LCNaCGl~~~ 66 (147)
..|.+|++..-=.|-- ++.-....|+.||-.|=
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyP 79 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYP 79 (158)
T ss_pred HHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCc
Confidence 4677777765444432 33334578999997643
No 78
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=22.38 E-value=19 Score=21.57 Aligned_cols=29 Identities=31% Similarity=0.614 Sum_probs=15.1
Q ss_pred ccccCCCCC-CCccccCCCCCcccchhHHH
Q 032112 35 TCADCGTTK-TPLWRGGPAGPKSLCNACGI 63 (147)
Q Consensus 35 ~C~nCgtt~-Tp~WR~gp~G~~~LCNaCGl 63 (147)
.|.+|++.- -+...=.+.|...-|-.||-
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCC
Confidence 466666652 34444444454555666654
No 79
>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=22.19 E-value=50 Score=19.72 Aligned_cols=17 Identities=35% Similarity=1.015 Sum_probs=12.9
Q ss_pred CCCCccccCCCCCcccchhH
Q 032112 42 TKTPLWRGGPAGPKSLCNAC 61 (147)
Q Consensus 42 t~Tp~WR~gp~G~~~LCNaC 61 (147)
..||.|-.+.... |+.|
T Consensus 19 ~~~p~W~~~~~~~---C~~C 35 (36)
T PF09698_consen 19 YTTPTWGSGATTA---CGSC 35 (36)
T ss_pred ccCceeCCCCCCc---cccc
Confidence 4578898887773 8887
No 80
>PHA00626 hypothetical protein
Probab=21.96 E-value=25 Score=23.85 Aligned_cols=33 Identities=24% Similarity=0.595 Sum_probs=21.0
Q ss_pred ccccCCCCCCCc--cccCCCCCcccchhHHHHHHhh
Q 032112 35 TCADCGTTKTPL--WRGGPAGPKSLCNACGIRSRKK 68 (147)
Q Consensus 35 ~C~nCgtt~Tp~--WR~gp~G~~~LCNaCGl~~~k~ 68 (147)
.|.+||..+-.. -=+++.. .+.|..||..+-+.
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 488999853221 0123444 48999999887753
No 81
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=21.65 E-value=29 Score=24.58 Aligned_cols=35 Identities=26% Similarity=0.628 Sum_probs=24.9
Q ss_pred CCCccccCCCCCCCcc----ccCCCCC--cccchhHHHHHH
Q 032112 32 IKKTCADCGTTKTPLW----RGGPAGP--KSLCNACGIRSR 66 (147)
Q Consensus 32 ~~~~C~nCgtt~Tp~W----R~gp~G~--~~LCNaCGl~~~ 66 (147)
....|.+||-.+.--| |...++. -+.|-.||..|+
T Consensus 61 ~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 61 TRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred ccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeE
Confidence 3579999997775444 5555553 368999998886
No 82
>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=21.61 E-value=79 Score=22.44 Aligned_cols=34 Identities=26% Similarity=0.467 Sum_probs=24.2
Q ss_pred CCCCccccCCCCCCCccccCCCCCcccchhHHHHHHhhc
Q 032112 31 SIKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKR 69 (147)
Q Consensus 31 ~~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~ 69 (147)
.+...|.-|+...+-.+ .| ...|+||..+++..-
T Consensus 4 ~~~~~C~VCg~~a~g~h----yG-v~sC~aCk~FFRR~v 37 (90)
T cd07169 4 AEQRTCLICGDRATGLH----YG-IISCEGCKGFFKRSI 37 (90)
T ss_pred ccCCCCeecCCcCcceE----EC-cceehhhHHHHHHHh
Confidence 34566999997655443 34 368999999998754
No 83
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=21.32 E-value=39 Score=31.36 Aligned_cols=35 Identities=23% Similarity=0.737 Sum_probs=26.4
Q ss_pred CccccCCCCCCCcccc-------CCCCCcccchhHHHHHHhh
Q 032112 34 KTCADCGTTKTPLWRG-------GPAGPKSLCNACGIRSRKK 68 (147)
Q Consensus 34 ~~C~nCgtt~Tp~WR~-------gp~G~~~LCNaCGl~~~k~ 68 (147)
-.|.||+.-..+.|.+ .+....+.|-.||-.+.-+
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~ 242 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEH 242 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHH
Confidence 5899999999998763 2444578999999766543
No 84
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=20.53 E-value=41 Score=28.08 Aligned_cols=33 Identities=24% Similarity=0.479 Sum_probs=23.1
Q ss_pred CCCccccCCCCCCCccccCCCCCcccchhHHHHHHhh
Q 032112 32 IKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKK 68 (147)
Q Consensus 32 ~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~ 68 (147)
..+.|..||+..... ..|....|.+||..+..+
T Consensus 98 ~~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~yp~ 130 (256)
T PRK00241 98 SHRFCGYCGHPMHPS----KTEWAMLCPHCRERYYPR 130 (256)
T ss_pred cCccccccCCCCeec----CCceeEECCCCCCEECCC
Confidence 357899999975542 334456899999776543
No 85
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.37 E-value=22 Score=22.93 Aligned_cols=29 Identities=24% Similarity=0.532 Sum_probs=20.2
Q ss_pred CCCccccCCCCCCCccccCCCCCcccchhHHHHH
Q 032112 32 IKKTCADCGTTKTPLWRGGPAGPKSLCNACGIRS 65 (147)
Q Consensus 32 ~~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~ 65 (147)
..+.|.+|+.. -++... + ...|..||..+
T Consensus 19 ~~~fCP~Cg~~--~m~~~~--~-r~~C~~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSG--FMAEHL--D-RWHCGKCGYTE 47 (50)
T ss_pred ccCcCcCCCcc--hheccC--C-cEECCCcCCEE
Confidence 45689999975 444443 3 47899999754
No 86
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=20.35 E-value=45 Score=29.35 Aligned_cols=32 Identities=31% Similarity=0.728 Sum_probs=21.4
Q ss_pred ccccCCCCCCCccccCCCCCcccchhHHHHHHh
Q 032112 35 TCADCGTTKTPLWRGGPAGPKSLCNACGIRSRK 67 (147)
Q Consensus 35 ~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k 67 (147)
.|..|....-.+--+-..|. ++|-.|||-...
T Consensus 2 ~c~~C~~~~~~~V~d~~~gd-tvC~~CGlVl~~ 33 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGD-TVCSECGLVLED 33 (308)
T ss_pred CCCCCCCCCCCeeeeccCCc-eecccCCeeecc
Confidence 47777766555666666674 788888876543
No 87
>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=20.23 E-value=37 Score=22.41 Aligned_cols=10 Identities=70% Similarity=1.408 Sum_probs=9.0
Q ss_pred CccccCCCCC
Q 032112 45 PLWRGGPAGP 54 (147)
Q Consensus 45 p~WR~gp~G~ 54 (147)
|.||.||.|-
T Consensus 34 ~E~R~G~~Gf 43 (54)
T PF12553_consen 34 PEWREGPAGF 43 (54)
T ss_pred HhheecCCCc
Confidence 8899999985
No 88
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=20.14 E-value=53 Score=24.96 Aligned_cols=41 Identities=22% Similarity=0.508 Sum_probs=27.8
Q ss_pred CCCCCCCCCccccCCCCCCCcc----ccCCCCC--cccchhHHHHHH
Q 032112 26 SSDENSIKKTCADCGTTKTPLW----RGGPAGP--KSLCNACGIRSR 66 (147)
Q Consensus 26 ~~~~~~~~~~C~nCgtt~Tp~W----R~gp~G~--~~LCNaCGl~~~ 66 (147)
+.=+....+.|.+|+-.+---+ |++...- -++|-.||-+|.
T Consensus 66 PTLPrts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~C~h~wt 112 (113)
T KOG2691|consen 66 PTLPRTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCSCGHRWT 112 (113)
T ss_pred CCcCccccccCCccCCcceEEEecccccccceEEEEEEecccccccc
Confidence 3445567889999999874433 4555542 368988998773
No 89
>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=20.13 E-value=95 Score=21.99 Aligned_cols=32 Identities=25% Similarity=0.419 Sum_probs=22.2
Q ss_pred CCccccCCCCCCCccccCCCCCcccchhHHHHHHhhc
Q 032112 33 KKTCADCGTTKTPLWRGGPAGPKSLCNACGIRSRKKR 69 (147)
Q Consensus 33 ~~~C~nCgtt~Tp~WR~gp~G~~~LCNaCGl~~~k~~ 69 (147)
...|.-|+...+-.+ .| ...|+||..+++...
T Consensus 6 ~~~C~VCg~~~~g~h----yG-v~sC~aCk~FFRR~v 37 (90)
T cd07168 6 PKLCSICEDKATGLH----YG-IITCEGCKGFFKRTV 37 (90)
T ss_pred CCCCcccCCcCcceE----EC-ceehhhhhHhhhhhh
Confidence 345999997554322 24 368999999998754
Done!