Query 024771
Match_columns 262
No_of_seqs 180 out of 747
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 07:18:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024771.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024771hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00202 ZnF_GATA Zinc finger D 99.5 3.8E-15 8.3E-20 107.5 3.6 44 178-224 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.5 8E-15 1.7E-19 104.8 3.7 40 175-214 2-41 (52)
3 PF00320 GATA: GATA zinc finge 99.5 8.5E-15 1.8E-19 97.6 0.6 35 179-213 1-35 (36)
4 KOG1601 GATA-4/5/6 transcripti 99.2 3.3E-11 7.1E-16 100.4 4.8 71 176-246 199-303 (340)
5 COG5641 GAT1 GATA Zn-finger-co 98.1 1.5E-06 3.3E-11 86.5 2.4 55 175-231 157-215 (498)
6 PRK12286 rpmF 50S ribosomal pr 79.9 1.3 2.8E-05 32.7 1.8 25 175-208 26-50 (57)
7 PF01783 Ribosomal_L32p: Ribos 79.2 0.46 1E-05 34.5 -0.6 25 175-209 25-49 (56)
8 KOG3554 Histone deacetylase co 78.0 1.5 3.3E-05 44.9 2.3 36 175-210 385-422 (693)
9 COG5641 GAT1 GATA Zn-finger-co 73.3 2.2 4.7E-05 43.4 2.1 37 176-212 297-334 (498)
10 PF14803 Nudix_N_2: Nudix N-te 68.9 1.2 2.7E-05 29.8 -0.5 30 177-206 1-30 (34)
11 PRK01110 rpmF 50S ribosomal pr 58.1 5.8 0.00012 29.5 1.3 23 176-208 27-49 (60)
12 PRK03988 translation initiatio 57.4 3.2 7E-05 35.4 -0.2 31 177-208 103-133 (138)
13 TIGR00311 aIF-2beta translatio 55.4 3.6 7.9E-05 34.9 -0.2 31 177-208 98-128 (133)
14 TIGR01031 rpmF_bact ribosomal 54.1 9.4 0.0002 27.9 1.8 23 175-206 25-47 (55)
15 COG5347 GTPase-activating prot 53.2 6.1 0.00013 38.1 0.9 36 172-209 16-51 (319)
16 smart00653 eIF2B_5 domain pres 52.9 4.3 9.3E-05 33.4 -0.1 29 177-206 81-109 (110)
17 PRK14892 putative transcriptio 50.0 8.8 0.00019 31.3 1.2 35 175-210 20-54 (99)
18 PRK12336 translation initiatio 49.6 5 0.00011 35.8 -0.2 32 177-209 99-130 (201)
19 KOG3740 Uncharacterized conser 48.7 14 0.0003 39.1 2.6 49 171-219 457-508 (706)
20 PF08271 TF_Zn_Ribbon: TFIIB z 48.0 5.4 0.00012 27.0 -0.2 31 177-210 1-31 (43)
21 PF01412 ArfGap: Putative GTPa 44.5 16 0.00036 29.5 2.0 36 173-210 10-45 (116)
22 PF07282 OrfB_Zn_ribbon: Putat 42.2 10 0.00022 27.4 0.5 33 172-208 24-56 (69)
23 PF06677 Auto_anti-p27: Sjogre 41.0 11 0.00024 26.2 0.4 26 175-205 16-41 (41)
24 PF01873 eIF-5_eIF-2B: Domain 39.0 8.3 0.00018 32.3 -0.5 29 177-206 94-122 (125)
25 smart00105 ArfGap Putative GTP 38.1 27 0.00059 28.1 2.4 35 175-211 2-36 (112)
26 PLN03114 ADP-ribosylation fact 37.8 18 0.00039 36.0 1.5 36 173-210 19-54 (395)
27 KOG0909 Peptide:N-glycanase [P 36.7 17 0.00036 37.1 1.1 49 176-242 161-220 (500)
28 COG3952 Predicted membrane pro 33.8 9.8 0.00021 32.0 -0.9 19 189-209 76-94 (113)
29 COG2816 NPY1 NTP pyrophosphohy 32.6 19 0.00041 34.4 0.7 31 175-209 110-140 (279)
30 TIGR00244 transcriptional regu 32.2 22 0.00049 31.1 1.0 33 177-209 1-39 (147)
31 PRK00420 hypothetical protein; 32.0 20 0.00043 29.9 0.6 30 175-209 22-51 (112)
32 PRK13130 H/ACA RNA-protein com 31.7 39 0.00085 25.1 2.1 48 176-242 5-52 (56)
33 PF04810 zf-Sec23_Sec24: Sec23 31.2 19 0.00042 24.3 0.4 32 176-207 2-33 (40)
34 PF12760 Zn_Tnp_IS1595: Transp 30.5 23 0.0005 24.3 0.7 27 177-206 19-45 (46)
35 KOG1598 Transcription initiati 28.5 30 0.00066 35.7 1.4 30 177-209 1-30 (521)
36 PF02701 zf-Dof: Dof domain, z 27.4 72 0.0016 24.5 2.9 43 175-217 4-49 (63)
37 KOG0703 Predicted GTPase-activ 26.0 27 0.00058 33.5 0.5 29 175-205 24-52 (287)
38 PF13248 zf-ribbon_3: zinc-rib 25.7 40 0.00086 20.8 1.1 23 177-207 3-25 (26)
39 smart00778 Prim_Zn_Ribbon Zinc 24.3 46 0.00099 22.7 1.3 29 177-206 4-33 (37)
40 PRK00423 tfb transcription ini 23.6 43 0.00093 31.5 1.4 10 234-243 99-108 (310)
41 COG0333 RpmF Ribosomal protein 23.4 36 0.00079 25.4 0.7 23 176-207 27-49 (57)
42 PF10083 DUF2321: Uncharacteri 23.2 41 0.00088 29.9 1.0 32 177-208 40-78 (158)
43 PRK00241 nudC NADH pyrophospha 23.1 29 0.00063 31.9 0.2 30 176-209 99-128 (256)
44 PF09297 zf-NADH-PPase: NADH p 23.0 13 0.00028 23.8 -1.6 29 176-208 3-31 (32)
45 PRK04023 DNA polymerase II lar 22.9 33 0.00071 38.3 0.5 12 174-185 624-635 (1121)
46 PF12773 DZR: Double zinc ribb 22.8 56 0.0012 22.2 1.5 29 175-208 11-39 (50)
47 PF01096 TFIIS_C: Transcriptio 22.7 13 0.00029 25.1 -1.6 32 178-209 2-39 (39)
48 PF11781 RRN7: RNA polymerase 22.5 36 0.00077 22.9 0.4 25 177-206 9-33 (36)
49 TIGR01385 TFSII transcription 22.1 38 0.00083 32.3 0.8 36 173-209 255-297 (299)
50 PLN03119 putative ADP-ribosyla 21.4 50 0.0011 34.9 1.4 35 173-209 20-54 (648)
51 PRK00464 nrdR transcriptional 21.1 44 0.00094 29.1 0.8 33 177-209 1-39 (154)
52 PLN03131 hypothetical protein; 21.0 52 0.0011 35.1 1.5 35 173-209 20-54 (705)
53 COG0675 Transposase and inacti 20.1 48 0.001 29.1 0.9 29 172-209 305-333 (364)
No 1
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.54 E-value=3.8e-15 Score=107.51 Aligned_cols=44 Identities=45% Similarity=0.998 Sum_probs=38.5
Q ss_pred ccccCCCCCCCCcccCCCCCcccchhhhhhhhhCCCCCCCCCCCCCC
Q 024771 178 KCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKSGRLVPEYRPANSPT 224 (262)
Q Consensus 178 ~C~nCgtt~TP~WRrGP~G~~tLCNACGL~ykk~rllp~yrpa~sPt 224 (262)
.|+||++++||+||+||.|..+|||||||||++++ .+||...+.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~---~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG---VMRPLSKRK 44 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC---CCCCcccCc
Confidence 59999999999999999888999999999999876 567766544
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.52 E-value=8e-15 Score=104.80 Aligned_cols=40 Identities=53% Similarity=1.136 Sum_probs=36.4
Q ss_pred CCcccccCCCCCCCCcccCCCCCcccchhhhhhhhhCCCC
Q 024771 175 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKSGRLV 214 (262)
Q Consensus 175 ~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~ykk~rll 214 (262)
..+.|+||++++||+||+||.|.++|||||||+|++++.+
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 4578999999999999999999889999999999976654
No 3
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.47 E-value=8.5e-15 Score=97.65 Aligned_cols=35 Identities=54% Similarity=1.216 Sum_probs=28.0
Q ss_pred cccCCCCCCCCcccCCCCCcccchhhhhhhhhCCC
Q 024771 179 CQHCGAEKTPQWRAGPMGPKTLCNACGVRFKSGRL 213 (262)
Q Consensus 179 C~nCgtt~TP~WRrGP~G~~tLCNACGL~ykk~rl 213 (262)
|+||++++||+||+||.|..+||||||++|++++.
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 89999999999999999988899999999998654
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=99.15 E-value=3.3e-11 Score=100.36 Aligned_cols=71 Identities=59% Similarity=1.176 Sum_probs=61.2
Q ss_pred CcccccCCCCCCCCcccCCCCCcccchhhhhhhhhC---CCCCCCCCCCCCC--------------CCcccccc------
Q 024771 176 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKSG---RLVPEYRPANSPT--------------FSSELHSN------ 232 (262)
Q Consensus 176 ~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~ykk~---rllp~yrpa~sPt--------------f~~~~hs~------ 232 (262)
...|.+|+++.||+||+++.|++.+|||||++|+++ +.++.++.+..++ +....|.+
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPRNVSPKGSGAVKGRTFTKSLHSNSAQLLL 278 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCccccccccCccccccccCCCccccccCCCCCcccccchhhhhh
Confidence 589999999999999999999999999999999988 8889999888877 44445554
Q ss_pred -----------chHHHHHHHHhhcc
Q 024771 233 -----------SHRKVVEMRRQKQM 246 (262)
Q Consensus 233 -----------~hrkv~~~Rkqk~~ 246 (262)
.+.++.++++.+..
T Consensus 279 ~~~~~~~~~~~~~~~~~~~~r~~~~ 303 (340)
T KOG1601|consen 279 APSKSEPPLLSSHQRVAEVRRYRES 303 (340)
T ss_pred hhcccCccccccchHHHHHhhccCc
Confidence 78888888887764
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.08 E-value=1.5e-06 Score=86.52 Aligned_cols=55 Identities=29% Similarity=0.513 Sum_probs=41.0
Q ss_pred CCcccccCCCCCCCCcccCCCC----CcccchhhhhhhhhCCCCCCCCCCCCCCCCccccc
Q 024771 175 IGRKCQHCGAEKTPQWRAGPMG----PKTLCNACGVRFKSGRLVPEYRPANSPTFSSELHS 231 (262)
Q Consensus 175 ~~r~C~nCgtt~TP~WRrGP~G----~~tLCNACGL~ykk~rllp~yrpa~sPtf~~~~hs 231 (262)
...+|.||.++.||+|||+..+ .-+|||||||+|+-++..-+ |...++...+.|.
T Consensus 157 ~~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~--P~t~ks~~~ks~~ 215 (498)
T COG5641 157 QPHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRA--PISLKSDSIKSRS 215 (498)
T ss_pred ccchhccccccCCccccccccccccCCccccccccccccccCCcCC--Ccccccccccccc
Confidence 3349999999999999999993 38999999999975554322 6665555444443
No 6
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=79.88 E-value=1.3 Score=32.71 Aligned_cols=25 Identities=32% Similarity=0.743 Sum_probs=19.4
Q ss_pred CCcccccCCCCCCCCcccCCCCCcccchhhhhhh
Q 024771 175 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRF 208 (262)
Q Consensus 175 ~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~y 208 (262)
..-.|.+||...-| +.+|..||.|.
T Consensus 26 ~l~~C~~CG~~~~~---------H~vC~~CG~Y~ 50 (57)
T PRK12286 26 GLVECPNCGEPKLP---------HRVCPSCGYYK 50 (57)
T ss_pred cceECCCCCCccCC---------eEECCCCCcCC
Confidence 34579999987655 89999999543
No 7
>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=79.25 E-value=0.46 Score=34.48 Aligned_cols=25 Identities=40% Similarity=0.919 Sum_probs=18.3
Q ss_pred CCcccccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 024771 175 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 209 (262)
Q Consensus 175 ~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~yk 209 (262)
....|.+||... -++.+|.+|| +|+
T Consensus 25 ~l~~c~~cg~~~---------~~H~vc~~cG-~y~ 49 (56)
T PF01783_consen 25 NLVKCPNCGEPK---------LPHRVCPSCG-YYK 49 (56)
T ss_dssp SEEESSSSSSEE---------STTSBCTTTB-BSS
T ss_pred ceeeeccCCCEe---------cccEeeCCCC-eEC
Confidence 346899999633 3479999999 554
No 8
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=77.97 E-value=1.5 Score=44.92 Aligned_cols=36 Identities=31% Similarity=0.681 Sum_probs=30.2
Q ss_pred CCcccccCCCCCCCCcc--cCCCCCcccchhhhhhhhh
Q 024771 175 IGRKCQHCGAEKTPQWR--AGPMGPKTLCNACGVRFKS 210 (262)
Q Consensus 175 ~~r~C~nCgtt~TP~WR--rGP~G~~tLCNACGL~ykk 210 (262)
.++.|.+|+|++.-+|- .+|+-.+.||-.|-+||||
T Consensus 385 ~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKK 422 (693)
T KOG3554|consen 385 DGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKK 422 (693)
T ss_pred CCCcccccccccccceeccCCCCccchhhHHHHHHHHH
Confidence 37899999999999993 3455556899999999997
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=73.33 E-value=2.2 Score=43.45 Aligned_cols=37 Identities=27% Similarity=0.408 Sum_probs=30.9
Q ss_pred CcccccCCC-CCCCCcccCCCCCcccchhhhhhhhhCC
Q 024771 176 GRKCQHCGA-EKTPQWRAGPMGPKTLCNACGVRFKSGR 212 (262)
Q Consensus 176 ~r~C~nCgt-t~TP~WRrGP~G~~tLCNACGL~ykk~r 212 (262)
...|.+|++ +.||.||+...-.-++|||||++.+..+
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~ 334 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPG 334 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCCcc
Confidence 457888887 7899999988777899999999998543
No 10
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=68.86 E-value=1.2 Score=29.78 Aligned_cols=30 Identities=27% Similarity=0.684 Sum_probs=16.4
Q ss_pred cccccCCCCCCCCcccCCCCCcccchhhhh
Q 024771 177 RKCQHCGAEKTPQWRAGPMGPKTLCNACGV 206 (262)
Q Consensus 177 r~C~nCgtt~TP~WRrGP~G~~tLCNACGL 206 (262)
+.|.+||..-+-.--.|.+-.+..|.+||-
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 369999987544444677778899999984
No 11
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=58.13 E-value=5.8 Score=29.50 Aligned_cols=23 Identities=13% Similarity=0.015 Sum_probs=16.9
Q ss_pred CcccccCCCCCCCCcccCCCCCcccchhhhhhh
Q 024771 176 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRF 208 (262)
Q Consensus 176 ~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~y 208 (262)
...|.+||...-| +.+|- ||.|.
T Consensus 27 ~~~c~~cg~~~~p---------H~vc~-cG~Y~ 49 (60)
T PRK01110 27 LSVDKTTGEYHLP---------HHVSP-KGYYK 49 (60)
T ss_pred eeEcCCCCceecc---------ceecC-CcccC
Confidence 4579999986544 67899 99554
No 12
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=57.38 E-value=3.2 Score=35.43 Aligned_cols=31 Identities=29% Similarity=0.617 Sum_probs=23.6
Q ss_pred cccccCCCCCCCCcccCCCCCcccchhhhhhh
Q 024771 177 RKCQHCGAEKTPQWRAGPMGPKTLCNACGVRF 208 (262)
Q Consensus 177 r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~y 208 (262)
-.|..|+...|-+=+++-. --.-|+|||-..
T Consensus 103 VlC~~C~spdT~l~k~~r~-~~l~C~ACGa~~ 133 (138)
T PRK03988 103 VICPECGSPDTKLIKEGRI-WVLKCEACGAET 133 (138)
T ss_pred EECCCCCCCCcEEEEcCCe-EEEEcccCCCCC
Confidence 4799999999999875332 146899999654
No 13
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=55.45 E-value=3.6 Score=34.90 Aligned_cols=31 Identities=26% Similarity=0.611 Sum_probs=23.3
Q ss_pred cccccCCCCCCCCcccCCCCCcccchhhhhhh
Q 024771 177 RKCQHCGAEKTPQWRAGPMGPKTLCNACGVRF 208 (262)
Q Consensus 177 r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~y 208 (262)
-.|..|+...|-+=+.+-. --.-|+|||-..
T Consensus 98 VlC~~C~sPdT~l~k~~r~-~~l~C~ACGa~~ 128 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRV-SLLKCEACGAKA 128 (133)
T ss_pred EECCCCCCCCcEEEEeCCe-EEEecccCCCCC
Confidence 4799999999998875321 135899999654
No 14
>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=54.09 E-value=9.4 Score=27.87 Aligned_cols=23 Identities=35% Similarity=0.801 Sum_probs=17.2
Q ss_pred CCcccccCCCCCCCCcccCCCCCcccchhhhh
Q 024771 175 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGV 206 (262)
Q Consensus 175 ~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL 206 (262)
..-.|.+||... -++.+|-.||.
T Consensus 25 ~l~~C~~cG~~~---------~~H~vc~~cG~ 47 (55)
T TIGR01031 25 TLVVCPNCGEFK---------LPHRVCPSCGY 47 (55)
T ss_pred cceECCCCCCcc---------cCeeECCccCe
Confidence 345699999754 34899999993
No 15
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=53.21 E-value=6.1 Score=38.06 Aligned_cols=36 Identities=31% Similarity=0.720 Sum_probs=30.9
Q ss_pred CCCCCcccccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 024771 172 KVIIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 209 (262)
Q Consensus 172 ~~~~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~yk 209 (262)
.....+.|++|++.. |+|-.=.-| -.||--|.--.+
T Consensus 16 ~~~~Nk~CaDCga~~-P~W~S~nlG-vfiCi~CagvHR 51 (319)
T COG5347 16 SDSSNKKCADCGAPN-PTWASVNLG-VFLCIDCAGVHR 51 (319)
T ss_pred hccccCccccCCCCC-CceEecccC-eEEEeecchhhh
Confidence 345678999999999 999999999 999999966554
No 16
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=52.93 E-value=4.3 Score=33.41 Aligned_cols=29 Identities=28% Similarity=0.592 Sum_probs=22.1
Q ss_pred cccccCCCCCCCCcccCCCCCcccchhhhh
Q 024771 177 RKCQHCGAEKTPQWRAGPMGPKTLCNACGV 206 (262)
Q Consensus 177 r~C~nCgtt~TP~WRrGP~G~~tLCNACGL 206 (262)
-.|..|+...|-+=+.+-.= -.-|+|||-
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 47999999999998873211 345999995
No 17
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=50.04 E-value=8.8 Score=31.29 Aligned_cols=35 Identities=17% Similarity=0.300 Sum_probs=23.0
Q ss_pred CCcccccCCCCCCCCcccCCCCCcccchhhhhhhhh
Q 024771 175 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKS 210 (262)
Q Consensus 175 ~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~ykk 210 (262)
..-.|.+|+.. +-.-..+-...+..|-.||.|+..
T Consensus 20 t~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGKV-SISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCCe-EeeeecCCCcceEECCCCCCccCE
Confidence 45679999953 322222223558999999999864
No 18
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=49.60 E-value=5 Score=35.81 Aligned_cols=32 Identities=25% Similarity=0.497 Sum_probs=24.6
Q ss_pred cccccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 024771 177 RKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 209 (262)
Q Consensus 177 r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~yk 209 (262)
-.|..|+...|-+=+.+..= -.-|+|||-..-
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 47999999999998763211 357999998764
No 19
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=48.67 E-value=14 Score=39.15 Aligned_cols=49 Identities=18% Similarity=0.386 Sum_probs=37.9
Q ss_pred cCCCCCcccccCCCCCCCCcccCCCC---CcccchhhhhhhhhCCCCCCCCC
Q 024771 171 SKVIIGRKCQHCGAEKTPQWRAGPMG---PKTLCNACGVRFKSGRLVPEYRP 219 (262)
Q Consensus 171 ~~~~~~r~C~nCgtt~TP~WRrGP~G---~~tLCNACGL~ykk~rllp~yrp 219 (262)
..+.....|..|.+.-||.|+.-+.+ .+.+|.+|-.--.|+.+--+..+
T Consensus 457 ~~a~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSnqkkAlK~ehT~ 508 (706)
T KOG3740|consen 457 TLATEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSNQKKALKVEHTN 508 (706)
T ss_pred cccCCchhhhhcccccccccccccccCcchHHHHHhhhhhcccccccccchH
Confidence 34566789999999999999988777 46899999877766665544433
No 20
>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=47.95 E-value=5.4 Score=27.03 Aligned_cols=31 Identities=26% Similarity=0.762 Sum_probs=19.4
Q ss_pred cccccCCCCCCCCcccCCCCCcccchhhhhhhhh
Q 024771 177 RKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKS 210 (262)
Q Consensus 177 r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~ykk 210 (262)
+.|.+|+.+. -.+- -..| ...|..||+-..-
T Consensus 1 m~Cp~Cg~~~-~~~D-~~~g-~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 1 MKCPNCGSKE-IVFD-PERG-ELVCPNCGLVLEE 31 (43)
T ss_dssp ESBTTTSSSE-EEEE-TTTT-EEEETTT-BBEE-
T ss_pred CCCcCCcCCc-eEEc-CCCC-eEECCCCCCEeec
Confidence 3689999866 2222 2345 7899999987653
No 21
>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=44.47 E-value=16 Score=29.47 Aligned_cols=36 Identities=31% Similarity=0.628 Sum_probs=25.4
Q ss_pred CCCCcccccCCCCCCCCcccCCCCCcccchhhhhhhhh
Q 024771 173 VIIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKS 210 (262)
Q Consensus 173 ~~~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~ykk 210 (262)
....+.|++|+... |.|-.=.-| -.||-.|.-..+.
T Consensus 10 ~~~N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~ 45 (116)
T PF01412_consen 10 KPGNKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRS 45 (116)
T ss_dssp STTCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHH
T ss_pred CcCcCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHH
Confidence 34578999999554 699998899 8999999988774
No 22
>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=42.22 E-value=10 Score=27.43 Aligned_cols=33 Identities=21% Similarity=0.603 Sum_probs=24.5
Q ss_pred CCCCCcccccCCCCCCCCcccCCCCCcccchhhhhhh
Q 024771 172 KVIIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRF 208 (262)
Q Consensus 172 ~~~~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~y 208 (262)
+......|..||...-- ...+....|..||..+
T Consensus 24 ~~~TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 24 EAYTSQTCPRCGHRNKK----RRSGRVFTCPNCGFEM 56 (69)
T ss_pred CCCCccCccCccccccc----ccccceEEcCCCCCEE
Confidence 44456789999986654 4455578999999876
No 23
>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=40.99 E-value=11 Score=26.23 Aligned_cols=26 Identities=38% Similarity=0.928 Sum_probs=20.2
Q ss_pred CCcccccCCCCCCCCcccCCCCCcccchhhh
Q 024771 175 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACG 205 (262)
Q Consensus 175 ~~r~C~nCgtt~TP~WRrGP~G~~tLCNACG 205 (262)
....|..| .||+.| ..+| +.+|-+|+
T Consensus 16 L~~~Cp~C---~~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 16 LDEHCPDC---GTPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred hcCccCCC---CCeeEE-ecCC-CEECCCCC
Confidence 45678888 589999 3466 79999986
No 24
>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=38.96 E-value=8.3 Score=32.35 Aligned_cols=29 Identities=31% Similarity=0.670 Sum_probs=23.3
Q ss_pred cccccCCCCCCCCcccCCCCCcccchhhhh
Q 024771 177 RKCQHCGAEKTPQWRAGPMGPKTLCNACGV 206 (262)
Q Consensus 177 r~C~nCgtt~TP~WRrGP~G~~tLCNACGL 206 (262)
-.|..|+..+|-+=+.+..= -.-|+|||-
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 46999999999998874433 578999994
No 25
>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=38.10 E-value=27 Score=28.06 Aligned_cols=35 Identities=34% Similarity=0.709 Sum_probs=29.6
Q ss_pred CCcccccCCCCCCCCcccCCCCCcccchhhhhhhhhC
Q 024771 175 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKSG 211 (262)
Q Consensus 175 ~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~ykk~ 211 (262)
.++.|++|+. .-|.|-.=.-| -.+|-.|.-..+.-
T Consensus 2 ~N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~l 36 (112)
T smart00105 2 GNKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRSL 36 (112)
T ss_pred CCCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHhc
Confidence 4678999998 55999998899 89999998887753
No 26
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=37.78 E-value=18 Score=36.04 Aligned_cols=36 Identities=28% Similarity=0.627 Sum_probs=30.0
Q ss_pred CCCCcccccCCCCCCCCcccCCCCCcccchhhhhhhhh
Q 024771 173 VIIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKS 210 (262)
Q Consensus 173 ~~~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~ykk 210 (262)
...++.|++|+... |.|-.=..| -.||-.|.=..+.
T Consensus 19 kPgNk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRs 54 (395)
T PLN03114 19 KSDNKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRS 54 (395)
T ss_pred CcCCCcCccCCCCC-CCceeeccc-eeehhhhhHhhcc
Confidence 34678999999865 999999999 8999999766653
No 27
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=36.69 E-value=17 Score=37.14 Aligned_cols=49 Identities=31% Similarity=0.651 Sum_probs=33.9
Q ss_pred CcccccCCCCC-CCCcccCCCCCc----------ccchhhhhhhhhCCCCCCCCCCCCCCCCccccccchHHHHHHHH
Q 024771 176 GRKCQHCGAEK-TPQWRAGPMGPK----------TLCNACGVRFKSGRLVPEYRPANSPTFSSELHSNSHRKVVEMRR 242 (262)
Q Consensus 176 ~r~C~nCgtt~-TP~WRrGP~G~~----------tLCNACGL~ykk~rllp~yrpa~sPtf~~~~hs~~hrkv~~~Rk 242 (262)
...|.+||... +++=+.+|.+.. +.||+||.--+ .|+| |...|+++.|+
T Consensus 161 ~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~R----FPRY--------------Ndp~kLLeTRk 220 (500)
T KOG0909|consen 161 NPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETR----FPRY--------------NDPIKLLETRK 220 (500)
T ss_pred CCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCccc----Cccc--------------CCHHHHHhhcc
Confidence 34799999877 555554554432 68999997654 3444 55788888887
No 28
>COG3952 Predicted membrane protein [Function unknown]
Probab=33.76 E-value=9.8 Score=32.00 Aligned_cols=19 Identities=32% Similarity=0.454 Sum_probs=15.3
Q ss_pred CcccCCCCCcccchhhhhhhh
Q 024771 189 QWRAGPMGPKTLCNACGVRFK 209 (262)
Q Consensus 189 ~WRrGP~G~~tLCNACGL~yk 209 (262)
.||.+|-+ .||+|||++-.
T Consensus 76 i~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HHhcchHH--HHHHhhhHHHH
Confidence 36777777 99999999864
No 29
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=32.64 E-value=19 Score=34.35 Aligned_cols=31 Identities=29% Similarity=0.630 Sum_probs=24.7
Q ss_pred CCcccccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 024771 175 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 209 (262)
Q Consensus 175 ~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~yk 209 (262)
..|.|..||+...|. ..|-+.+|+.||.++.
T Consensus 110 ~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~f 140 (279)
T COG2816 110 SHRFCGRCGTKTYPR----EGGWARVCPKCGHEHF 140 (279)
T ss_pred hCcCCCCCCCcCccc----cCceeeeCCCCCCccC
Confidence 357899999988773 3566799999998874
No 30
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=32.21 E-value=22 Score=31.06 Aligned_cols=33 Identities=27% Similarity=0.516 Sum_probs=25.1
Q ss_pred cccccCCCCCCCCc--ccCCCC----Ccccchhhhhhhh
Q 024771 177 RKCQHCGAEKTPQW--RAGPMG----PKTLCNACGVRFK 209 (262)
Q Consensus 177 r~C~nCgtt~TP~W--RrGP~G----~~tLCNACGL~yk 209 (262)
+.|..|+...|-.- |...+| .+--|.+||.+|-
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccc
Confidence 47999999888775 555555 3468999999985
No 31
>PRK00420 hypothetical protein; Validated
Probab=32.04 E-value=20 Score=29.95 Aligned_cols=30 Identities=23% Similarity=0.697 Sum_probs=23.7
Q ss_pred CCcccccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 024771 175 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 209 (262)
Q Consensus 175 ~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~yk 209 (262)
....|..|| +|+.|- ..| +..|-+||..+.
T Consensus 22 l~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCC---Ccceec-CCC-ceECCCCCCeee
Confidence 456788888 688874 356 899999999885
No 32
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=31.74 E-value=39 Score=25.07 Aligned_cols=48 Identities=35% Similarity=0.679 Sum_probs=31.2
Q ss_pred CcccccCCCCCCCCcccCCCCCcccchhhhhhhhhCCCCCCCCCCCCCCCCccccccchHHHHHHHH
Q 024771 176 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKSGRLVPEYRPANSPTFSSELHSNSHRKVVEMRR 242 (262)
Q Consensus 176 ~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~ykk~rllp~yrpa~sPtf~~~~hs~~hrkv~~~Rk 242 (262)
-+.|..|++.+- +..|-.||.... .+..|.|++.-.-..+|..+++|.
T Consensus 5 mr~C~~CgvYTL----------k~~CP~CG~~t~---------~~~P~rfSp~D~y~~yR~~~kk~~ 52 (56)
T PRK13130 5 IRKCPKCGVYTL----------KEICPVCGGKTK---------NPHPPRFSPEDKYGKYRRALKKRR 52 (56)
T ss_pred ceECCCCCCEEc----------cccCcCCCCCCC---------CCCCCCCCCCCccHHHHHHHHHHh
Confidence 357888887654 466777776542 344566777776667776666654
No 33
>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=31.24 E-value=19 Score=24.26 Aligned_cols=32 Identities=28% Similarity=0.621 Sum_probs=21.3
Q ss_pred CcccccCCCCCCCCcccCCCCCcccchhhhhh
Q 024771 176 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVR 207 (262)
Q Consensus 176 ~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~ 207 (262)
..+|.+|++---|.-+-...|....||-|+..
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 35799999999898888888888999999874
No 34
>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=30.53 E-value=23 Score=24.32 Aligned_cols=27 Identities=30% Similarity=0.624 Sum_probs=19.8
Q ss_pred cccccCCCCCCCCcccCCCCCcccchhhhh
Q 024771 177 RKCQHCGAEKTPQWRAGPMGPKTLCNACGV 206 (262)
Q Consensus 177 r~C~nCgtt~TP~WRrGP~G~~tLCNACGL 206 (262)
..|.+||.+ ..-|-++ .+ ..-|++|+-
T Consensus 19 ~~CP~Cg~~-~~~~~~~-~~-~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-KHYRLKT-RG-RYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-eeEEeCC-CC-eEECCCCCC
Confidence 569999998 5555554 34 789999974
No 35
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=28.50 E-value=30 Score=35.70 Aligned_cols=30 Identities=30% Similarity=0.793 Sum_probs=21.2
Q ss_pred cccccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 024771 177 RKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 209 (262)
Q Consensus 177 r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~yk 209 (262)
+.|.||+.+. +. |+-..| ...|.|||.-.-
T Consensus 1 ~~C~~C~~s~-fe-~d~a~g-~~~C~~CG~v~E 30 (521)
T KOG1598|consen 1 MVCKNCGGSN-FE-RDEATG-NLYCTACGTVLE 30 (521)
T ss_pred CcCCCCCCCC-cc-cccccC-Cceeccccceee
Confidence 4799999864 22 222455 899999998764
No 36
>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=27.43 E-value=72 Score=24.50 Aligned_cols=43 Identities=16% Similarity=0.390 Sum_probs=32.3
Q ss_pred CCcccccCCCCCCCCc---ccCCCCCcccchhhhhhhhhCCCCCCC
Q 024771 175 IGRKCQHCGAEKTPQW---RAGPMGPKTLCNACGVRFKSGRLVPEY 217 (262)
Q Consensus 175 ~~r~C~nCgtt~TP~W---RrGP~G~~tLCNACGL~ykk~rllp~y 217 (262)
....|..|..+.|--= --...-|+..|-+|-.+|..++.+...
T Consensus 4 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnV 49 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNV 49 (63)
T ss_pred cCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCC
Confidence 4568999999887652 222345689999999999998887554
No 37
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=26.01 E-value=27 Score=33.54 Aligned_cols=29 Identities=31% Similarity=0.885 Sum_probs=25.6
Q ss_pred CCcccccCCCCCCCCcccCCCCCcccchhhh
Q 024771 175 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACG 205 (262)
Q Consensus 175 ~~r~C~nCgtt~TP~WRrGP~G~~tLCNACG 205 (262)
..+.|++|++. .|.|-.=.-| -.+|=.|-
T Consensus 24 ~N~~CADC~a~-~P~WaSwnlG-vFiC~~C~ 52 (287)
T KOG0703|consen 24 DNKVCADCGAK-GPRWASWNLG-VFICLRCA 52 (287)
T ss_pred ccCcccccCCC-CCCeEEeecC-eEEEeecc
Confidence 37899999999 9999998899 89998874
No 38
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=25.66 E-value=40 Score=20.79 Aligned_cols=23 Identities=35% Similarity=0.870 Sum_probs=14.8
Q ss_pred cccccCCCCCCCCcccCCCCCcccchhhhhh
Q 024771 177 RKCQHCGAEKTPQWRAGPMGPKTLCNACGVR 207 (262)
Q Consensus 177 r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~ 207 (262)
+.|.+||.... .+ ...|-.||..
T Consensus 3 ~~Cp~Cg~~~~-------~~-~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEID-------PD-AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCC-------cc-cccChhhCCC
Confidence 56888887542 22 5677777753
No 39
>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=24.35 E-value=46 Score=22.74 Aligned_cols=29 Identities=24% Similarity=0.715 Sum_probs=20.7
Q ss_pred cccccCCCCCCCCcccC-CCCCcccchhhhh
Q 024771 177 RKCQHCGAEKTPQWRAG-PMGPKTLCNACGV 206 (262)
Q Consensus 177 r~C~nCgtt~TP~WRrG-P~G~~tLCNACGL 206 (262)
..|-.|+....=.|..- ..| ...|+.||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G-~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRG-TWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCc-CEEeCCCCC
Confidence 46899998776667543 234 789999973
No 40
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=23.64 E-value=43 Score=31.46 Aligned_cols=10 Identities=10% Similarity=0.338 Sum_probs=4.7
Q ss_pred hHHHHHHHHh
Q 024771 234 HRKVVEMRRQ 243 (262)
Q Consensus 234 hrkv~~~Rkq 243 (262)
+++.+++|+.
T Consensus 99 ~~~~~rl~~~ 108 (310)
T PRK00423 99 RAQLYRLRKW 108 (310)
T ss_pred HHHHHHHHHH
Confidence 3444555543
No 41
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=23.41 E-value=36 Score=25.41 Aligned_cols=23 Identities=35% Similarity=0.820 Sum_probs=14.8
Q ss_pred CcccccCCCCCCCCcccCCCCCcccchhhhhh
Q 024771 176 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVR 207 (262)
Q Consensus 176 ~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~ 207 (262)
.-.|.+||...= ++.+|-.||.|
T Consensus 27 ~~~c~~cG~~~l---------~Hrvc~~cg~Y 49 (57)
T COG0333 27 LSVCPNCGEYKL---------PHRVCLKCGYY 49 (57)
T ss_pred ceeccCCCCccc---------CceEcCCCCCc
Confidence 456888876543 25777777743
No 42
>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=23.20 E-value=41 Score=29.90 Aligned_cols=32 Identities=19% Similarity=0.676 Sum_probs=22.6
Q ss_pred cccccCCCCCCCCccc-------CCCCCcccchhhhhhh
Q 024771 177 RKCQHCGAEKTPQWRA-------GPMGPKTLCNACGVRF 208 (262)
Q Consensus 177 r~C~nCgtt~TP~WRr-------GP~G~~tLCNACGL~y 208 (262)
..|.+|++..--.|-- ++.-....|+.||..|
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCC
Confidence 4688888766555522 4444567899999998
No 43
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=23.09 E-value=29 Score=31.90 Aligned_cols=30 Identities=30% Similarity=0.593 Sum_probs=22.1
Q ss_pred CcccccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 024771 176 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 209 (262)
Q Consensus 176 ~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~yk 209 (262)
.+.|..||...... ..|.+..|.+||..+-
T Consensus 99 ~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 99 HRFCGYCGHPMHPS----KTEWAMLCPHCRERYY 128 (256)
T ss_pred CccccccCCCCeec----CCceeEECCCCCCEEC
Confidence 46899999975542 3566788999997653
No 44
>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=22.99 E-value=13 Score=23.81 Aligned_cols=29 Identities=38% Similarity=0.801 Sum_probs=15.6
Q ss_pred CcccccCCCCCCCCcccCCCCCcccchhhhhhh
Q 024771 176 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRF 208 (262)
Q Consensus 176 ~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~y 208 (262)
.+.|..||....+. +.|....|.+||..+
T Consensus 3 ~rfC~~CG~~t~~~----~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA----PGGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--BEEE-----SSSS-EEESSSS-EE
T ss_pred CcccCcCCccccCC----CCcCEeECCCCcCEe
Confidence 36788888866543 245678888888753
No 45
>PRK04023 DNA polymerase II large subunit; Validated
Probab=22.91 E-value=33 Score=38.31 Aligned_cols=12 Identities=58% Similarity=1.077 Sum_probs=6.0
Q ss_pred CCCcccccCCCC
Q 024771 174 IIGRKCQHCGAE 185 (262)
Q Consensus 174 ~~~r~C~nCgtt 185 (262)
...+.|..||..
T Consensus 624 Vg~RfCpsCG~~ 635 (1121)
T PRK04023 624 IGRRKCPSCGKE 635 (1121)
T ss_pred ccCccCCCCCCc
Confidence 344555555544
No 46
>PF12773 DZR: Double zinc ribbon
Probab=22.80 E-value=56 Score=22.20 Aligned_cols=29 Identities=31% Similarity=0.734 Sum_probs=19.2
Q ss_pred CCcccccCCCCCCCCcccCCCCCcccchhhhhhh
Q 024771 175 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRF 208 (262)
Q Consensus 175 ~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~y 208 (262)
..+.|.+||+.-. ........|..||-..
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGAEN 39 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcCCC
Confidence 3567888888766 3344457788887654
No 47
>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=22.67 E-value=13 Score=25.07 Aligned_cols=32 Identities=28% Similarity=0.733 Sum_probs=17.7
Q ss_pred ccccCCCCCCCCc----ccCCCCCc--ccchhhhhhhh
Q 024771 178 KCQHCGAEKTPQW----RAGPMGPK--TLCNACGVRFK 209 (262)
Q Consensus 178 ~C~nCgtt~TP~W----RrGP~G~~--tLCNACGL~yk 209 (262)
.|..|+..++--| |.+.++.- ..|..||-+|+
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 4777887664443 55555522 46888887663
No 48
>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=22.52 E-value=36 Score=22.90 Aligned_cols=25 Identities=32% Similarity=0.864 Sum_probs=19.3
Q ss_pred cccccCCCCCCCCcccCCCCCcccchhhhh
Q 024771 177 RKCQHCGAEKTPQWRAGPMGPKTLCNACGV 206 (262)
Q Consensus 177 r~C~nCgtt~TP~WRrGP~G~~tLCNACGL 206 (262)
..|..|+.. |=...+| ...|..||-
T Consensus 9 ~~C~~C~~~----~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCC-EEEhhhCce
Confidence 459999887 5555678 899999984
No 49
>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=22.14 E-value=38 Score=32.29 Aligned_cols=36 Identities=28% Similarity=0.540 Sum_probs=25.7
Q ss_pred CCCCcccccCCCCCCCCc----ccCCCCCc---ccchhhhhhhh
Q 024771 173 VIIGRKCQHCGAEKTPQW----RAGPMGPK---TLCNACGVRFK 209 (262)
Q Consensus 173 ~~~~r~C~nCgtt~TP~W----RrGP~G~~---tLCNACGL~yk 209 (262)
.+....|..|+-...-.| |...++ - +.|..||-+|+
T Consensus 255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEp-mT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 255 VTDLFTCGKCKQKKCTYYQLQTRSADEP-MTTFVTCEECGNRWK 297 (299)
T ss_pred CcccccCCCCCCccceEEEecccCCCCC-CeEEEEcCCCCCeee
Confidence 445679999998776555 433333 3 38999999986
No 50
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=21.39 E-value=50 Score=34.89 Aligned_cols=35 Identities=23% Similarity=0.515 Sum_probs=28.8
Q ss_pred CCCCcccccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 024771 173 VIIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 209 (262)
Q Consensus 173 ~~~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~yk 209 (262)
....+.|++|+... |.|-.=.-| -.+|-.|.=..+
T Consensus 20 lPgNk~CADCgs~~-P~WASiNlG-IFICi~CSGIHR 54 (648)
T PLN03119 20 LPPNRRCINCNSLG-PQYVCTTFW-TFVCMACSGIHR 54 (648)
T ss_pred CcCCCccccCCCCC-CCceeeccc-eEEeccchhhhc
Confidence 45678999999866 999998899 899999965543
No 51
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=21.14 E-value=44 Score=29.10 Aligned_cols=33 Identities=33% Similarity=0.693 Sum_probs=22.1
Q ss_pred cccccCCCCCCCCcccC--CCC----Ccccchhhhhhhh
Q 024771 177 RKCQHCGAEKTPQWRAG--PMG----PKTLCNACGVRFK 209 (262)
Q Consensus 177 r~C~nCgtt~TP~WRrG--P~G----~~tLCNACGL~yk 209 (262)
+.|.+||...|-.--.- +.| ...-|.+||-.|.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~ 39 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFT 39 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcce
Confidence 46999998876653221 123 2367999999884
No 52
>PLN03131 hypothetical protein; Provisional
Probab=21.02 E-value=52 Score=35.08 Aligned_cols=35 Identities=20% Similarity=0.493 Sum_probs=28.8
Q ss_pred CCCCcccccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 024771 173 VIIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 209 (262)
Q Consensus 173 ~~~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~yk 209 (262)
...++.|++|+... |.|-.-.-| -.+|-.|.=..+
T Consensus 20 ~PgNk~CADCga~~-P~WASiNlG-IFICi~CSGIHR 54 (705)
T PLN03131 20 LPPNRRCINCNSLG-PQFVCTNFW-TFICMTCSGIHR 54 (705)
T ss_pred CcCCCccccCCCCC-CCeeEeccc-eEEchhchhhhc
Confidence 45678999999855 999998889 899999975554
No 53
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.13 E-value=48 Score=29.13 Aligned_cols=29 Identities=24% Similarity=0.572 Sum_probs=23.1
Q ss_pred CCCCCcccccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 024771 172 KVIIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 209 (262)
Q Consensus 172 ~~~~~r~C~nCgtt~TP~WRrGP~G~~tLCNACGL~yk 209 (262)
.......|..||. ..+....|..||..+.
T Consensus 305 ~~~tS~~C~~cg~---------~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 305 PYYTSKTCPCCGH---------LSGRLFKCPRCGFVHD 333 (364)
T ss_pred CCCCcccccccCC---------ccceeEECCCCCCeeh
Confidence 4667799999999 4465789999998653
Done!