Query 026433
Match_columns 238
No_of_seqs 166 out of 744
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 07:57:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026433.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026433hhsearch_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 7.8E-15 1.7E-19 104.6 3.0 44 154-200 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.5 1.3E-14 2.8E-19 102.5 3.5 40 151-190 2-41 (52)
3 PF00320 GATA: GATA zinc finge 99.4 1.5E-14 3.1E-19 95.3 -0.0 35 155-189 1-35 (36)
4 KOG1601 GATA-4/5/6 transcripti 99.1 7.4E-11 1.6E-15 96.8 4.8 71 152-222 199-303 (340)
5 COG5641 GAT1 GATA Zn-finger-co 97.9 4.2E-06 9.2E-11 82.3 2.3 54 152-207 158-215 (498)
6 KOG3554 Histone deacetylase co 90.8 0.18 3.9E-06 50.7 2.8 39 151-189 385-426 (693)
7 PF01783 Ribosomal_L32p: Ribos 81.8 0.41 8.8E-06 34.3 -0.2 48 109-185 2-49 (56)
8 PRK12286 rpmF 50S ribosomal pr 80.6 1.6 3.4E-05 31.8 2.5 49 108-184 2-50 (57)
9 PF14803 Nudix_N_2: Nudix N-te 73.7 0.96 2.1E-05 29.9 -0.2 30 153-182 1-30 (34)
10 COG5641 GAT1 GATA Zn-finger-co 70.5 3.1 6.7E-05 41.8 2.4 35 152-186 297-332 (498)
11 PRK03988 translation initiatio 64.1 2.4 5.2E-05 35.7 0.2 31 153-184 103-133 (138)
12 TIGR01031 rpmF_bact ribosomal 62.8 6.9 0.00015 28.2 2.3 23 152-183 26-48 (55)
13 TIGR00311 aIF-2beta translatio 61.9 2.6 5.7E-05 35.3 0.0 31 153-184 98-128 (133)
14 smart00653 eIF2B_5 domain pres 59.8 3.1 6.8E-05 33.7 0.1 29 153-182 81-109 (110)
15 PRK12336 translation initiatio 56.5 3.8 8.2E-05 36.1 0.1 32 153-185 99-130 (201)
16 PF08271 TF_Zn_Ribbon: TFIIB z 52.2 4.5 9.8E-05 27.0 -0.1 30 154-186 2-31 (43)
17 PRK01110 rpmF 50S ribosomal pr 51.4 10 0.00022 27.8 1.7 48 108-184 2-49 (60)
18 PRK14892 putative transcriptio 50.1 11 0.00024 30.3 1.8 35 151-186 20-54 (99)
19 COG5347 GTPase-activating prot 49.2 7.8 0.00017 36.8 0.9 35 150-186 18-52 (319)
20 PF07282 OrfB_Zn_ribbon: Putat 48.7 9 0.00019 27.3 1.0 34 148-185 24-57 (69)
21 TIGR00244 transcriptional regu 48.5 9.7 0.00021 32.8 1.3 34 153-186 1-40 (147)
22 PRK13130 H/ACA RNA-protein com 47.7 23 0.0005 25.9 3.0 49 152-219 5-53 (56)
23 KOG3740 Uncharacterized conser 46.3 10 0.00022 39.6 1.2 45 146-190 456-503 (706)
24 PF01873 eIF-5_eIF-2B: Domain 45.8 6.2 0.00013 32.7 -0.3 29 153-182 94-122 (125)
25 PF06677 Auto_anti-p27: Sjogre 44.6 10 0.00022 26.0 0.7 26 151-181 16-41 (41)
26 PF01412 ArfGap: Putative GTPa 41.3 16 0.00035 29.1 1.5 35 150-186 11-45 (116)
27 smart00105 ArfGap Putative GTP 38.4 17 0.00037 28.8 1.2 33 152-186 3-35 (112)
28 PLN03114 ADP-ribosylation fact 37.5 18 0.00039 35.6 1.4 35 150-186 20-54 (395)
29 COG2816 NPY1 NTP pyrophosphohy 37.2 16 0.00036 34.3 1.1 30 152-185 111-140 (279)
30 PF04810 zf-Sec23_Sec24: Sec23 35.6 17 0.00037 24.2 0.7 32 152-183 2-33 (40)
31 PRK00420 hypothetical protein; 35.1 19 0.00042 29.6 1.0 31 151-186 22-52 (112)
32 PF01096 TFIIS_C: Transcriptio 32.9 9.1 0.0002 25.5 -1.0 32 154-185 2-39 (39)
33 COG3529 Predicted nucleic-acid 32.4 9.1 0.0002 29.0 -1.1 35 151-185 9-43 (66)
34 PF09526 DUF2387: Probable met 31.9 14 0.00031 27.9 -0.1 36 151-186 7-42 (71)
35 PF09297 zf-NADH-PPase: NADH p 31.3 10 0.00022 23.9 -0.9 29 152-184 3-31 (32)
36 PRK04023 DNA polymerase II lar 31.2 22 0.00048 39.1 1.0 20 219-238 703-722 (1121)
37 KOG0909 Peptide:N-glycanase [P 31.1 27 0.00059 35.2 1.6 49 153-219 162-221 (500)
38 PF12773 DZR: Double zinc ribb 29.5 39 0.00084 22.6 1.7 30 151-185 11-40 (50)
39 PF12760 Zn_Tnp_IS1595: Transp 29.2 28 0.0006 23.6 0.9 27 153-182 19-45 (46)
40 PF13248 zf-ribbon_3: zinc-rib 28.5 34 0.00075 20.7 1.1 23 153-183 3-25 (26)
41 smart00778 Prim_Zn_Ribbon Zinc 28.5 38 0.00083 22.8 1.4 29 153-182 4-33 (37)
42 PRK00464 nrdR transcriptional 28.2 30 0.00065 29.7 1.1 34 153-186 1-40 (154)
43 KOG1598 Transcription initiati 27.7 33 0.00072 35.0 1.5 31 153-186 1-31 (521)
44 PF02701 zf-Dof: Dof domain, z 27.5 57 0.0012 24.7 2.4 43 151-193 4-49 (63)
45 PRK00423 tfb transcription ini 26.6 40 0.00087 31.2 1.8 11 150-160 28-38 (310)
46 PRK00241 nudC NADH pyrophospha 26.4 28 0.00061 31.5 0.7 30 152-185 99-128 (256)
47 PF14122 YokU: YokU-like prote 26.3 25 0.00054 28.1 0.3 34 154-187 1-48 (87)
48 PF11781 RRN7: RNA polymerase 25.5 30 0.00064 23.0 0.5 25 153-182 9-33 (36)
49 PF13717 zinc_ribbon_4: zinc-r 25.2 26 0.00056 23.0 0.2 31 154-184 4-35 (36)
50 COG0333 RpmF Ribosomal protein 24.1 44 0.00096 24.6 1.2 23 152-183 27-49 (57)
51 smart00661 RPOL9 RNA polymeras 23.6 51 0.0011 22.0 1.4 30 154-185 2-31 (52)
52 TIGR01385 TFSII transcription 23.4 41 0.00089 31.6 1.2 36 149-185 255-297 (299)
53 PRK00085 recO DNA repair prote 22.8 41 0.00089 29.2 1.0 29 152-181 149-177 (247)
54 PF04161 Arv1: Arv1-like famil 22.8 43 0.00094 29.3 1.2 34 153-186 1-36 (208)
55 PF10083 DUF2321: Uncharacteri 22.8 44 0.00095 29.3 1.2 32 153-184 40-78 (158)
56 COG1327 Predicted transcriptio 22.4 47 0.001 29.1 1.3 34 153-186 1-40 (156)
57 COG0675 Transposase and inacti 22.3 49 0.0011 28.6 1.4 29 148-185 305-333 (364)
58 PF09723 Zn-ribbon_8: Zinc rib 22.2 33 0.00072 23.0 0.3 28 154-182 7-34 (42)
59 KOG0703 Predicted GTPase-activ 22.0 38 0.00082 32.1 0.7 29 152-182 25-53 (287)
60 COG3952 Predicted membrane pro 21.7 22 0.00048 29.5 -0.8 18 166-185 77-94 (113)
61 PF05876 Terminase_GpA: Phage 21.1 46 0.001 33.5 1.1 35 151-185 199-240 (557)
62 PF09538 FYDLN_acid: Protein o 21.0 74 0.0016 25.8 2.1 15 171-185 6-20 (108)
63 PLN03119 putative ADP-ribosyla 20.7 54 0.0012 34.2 1.5 35 149-185 20-54 (648)
64 PRK14714 DNA polymerase II lar 20.6 44 0.00094 37.6 0.9 20 219-238 750-769 (1337)
65 PF03833 PolC_DP2: DNA polymer 20.3 34 0.00074 36.9 0.0 21 218-238 731-751 (900)
66 PLN03131 hypothetical protein; 20.0 57 0.0012 34.4 1.5 35 149-185 20-54 (705)
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=99.51 E-value=7.8e-15 Score=104.57 Aligned_cols=44 Identities=45% Similarity=0.998 Sum_probs=38.6
Q ss_pred eeccCCCCCCCCcccCCCCCcccchhhhhhhhcCCCCCCCCCCCCCC
Q 026433 154 KCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKSGRLVPEYRPANSPT 200 (238)
Q Consensus 154 ~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ykk~rllp~yrpa~sPt 200 (238)
.|+||++++||+||+||+|..+||||||++|++++ .+||...+.
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 49999999999999999998999999999999876 567766554
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.50 E-value=1.3e-14 Score=102.46 Aligned_cols=40 Identities=53% Similarity=1.136 Sum_probs=36.1
Q ss_pred CCceeccCCCCCCCCcccCCCCCcccchhhhhhhhcCCCC
Q 026433 151 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKSGRLV 190 (238)
Q Consensus 151 ~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ykk~rll 190 (238)
..+.|+||++++||+||+||.|..+|||||||+|++.+.+
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 3578999999999999999999889999999999985543
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=99.44 E-value=1.5e-14 Score=95.33 Aligned_cols=35 Identities=54% Similarity=1.216 Sum_probs=27.9
Q ss_pred eccCCCCCCCCcccCCCCCcccchhhhhhhhcCCC
Q 026433 155 CQHCGAEKTPQWRAGPMGPKTLCNACGVRFKSGRL 189 (238)
Q Consensus 155 C~nCgtt~TP~WRrGP~G~~~LCNACGL~ykk~rl 189 (238)
|.||++++||+||+||.|..+||||||++|++++.
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=99.11 E-value=7.4e-11 Score=96.84 Aligned_cols=71 Identities=59% Similarity=1.176 Sum_probs=61.5
Q ss_pred CceeccCCCCCCCCcccCCCCCcccchhhhhhhhcC---CCCCCCCCCCCCC--------------CCcccccc------
Q 026433 152 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKSG---RLVPEYRPANSPT--------------FSSELHSN------ 208 (238)
Q Consensus 152 ~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ykk~---rllp~yrpa~sPt--------------f~~~~hsn------ 208 (238)
...|.+|+++.||+||+++.|++.+|||||++|+++ +.++.++.+..++ +....|.+
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPRNVSPKGSGAVKGRTFTKSLHSNSAQLLL 278 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCccccccccCccccccccCCCccccccCCCCCcccccchhhhhh
Confidence 589999999999999999999999999999999997 7888999888877 44455555
Q ss_pred -----------hhHHHHHHHHhccc
Q 026433 209 -----------SHRKVVEMRRQKQM 222 (238)
Q Consensus 209 -----------~hrkv~~~R~qk~~ 222 (238)
.|.++.++++.+..
T Consensus 279 ~~~~~~~~~~~~~~~~~~~~r~~~~ 303 (340)
T KOG1601|consen 279 APSKSEPPLLSSHQRVAEVRRYRES 303 (340)
T ss_pred hhcccCccccccchHHHHHhhccCc
Confidence 78889988888764
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=97.93 E-value=4.2e-06 Score=82.30 Aligned_cols=54 Identities=30% Similarity=0.534 Sum_probs=42.3
Q ss_pred CceeccCCCCCCCCcccCCCC----CcccchhhhhhhhcCCCCCCCCCCCCCCCCccccc
Q 026433 152 GRKCQHCGAEKTPQWRAGPMG----PKTLCNACGVRFKSGRLVPEYRPANSPTFSSELHS 207 (238)
Q Consensus 152 ~r~C~nCgtt~TP~WRrGP~G----~~~LCNACGL~ykk~rllp~yrpa~sPtf~~~~hs 207 (238)
...|.||.++.||+|||+..+ .-+|||||||+|+-++..-+ |...++...+-|.
T Consensus 158 ~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~--P~t~ks~~~ks~~ 215 (498)
T COG5641 158 PHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRA--PISLKSDSIKSRS 215 (498)
T ss_pred cchhccccccCCccccccccccccCCccccccccccccccCCcCC--Ccccccccccccc
Confidence 448999999999999999993 38999999999987665432 6666666655544
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=90.82 E-value=0.18 Score=50.72 Aligned_cols=39 Identities=33% Similarity=0.712 Sum_probs=33.1
Q ss_pred CCceeccCCCCCCCCc--ccCCCCCcccchhhhhhhhc-CCC
Q 026433 151 IGRKCQHCGAEKTPQW--RAGPMGPKTLCNACGVRFKS-GRL 189 (238)
Q Consensus 151 ~~r~C~nCgtt~TP~W--RrGP~G~~~LCNACGL~ykk-~rl 189 (238)
.++.|.+|++++.-+| .-+|+..+.||-.|-++|+| +++
T Consensus 385 ~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 385 DGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred CCCcccccccccccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 4789999999999999 55667777999999999998 444
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=81.76 E-value=0.41 Score=34.29 Aligned_cols=48 Identities=42% Similarity=0.743 Sum_probs=27.2
Q ss_pred CCCCCCCCCccccccccccccccccCcCCCcCCCCCCCcCCCCCceeccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 026433 109 VPVRARSKLRTRCRRELLNQEAWWGSVHGSVKAAKPVVSKVIIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 185 (238)
Q Consensus 109 vP~raRSKR~R~~~~~~~~~~~~~~~~~~~~kk~k~~~~~~~~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~yk 185 (238)
||-++.|+.+++.++. -|.+.. .....|.+||... -++.+|.+|| +|+
T Consensus 2 vPKrk~Sksr~~~Rrs-----~~~l~~--------------~~l~~c~~cg~~~---------~~H~vc~~cG-~y~ 49 (56)
T PF01783_consen 2 VPKRKTSKSRKRMRRS-----HWKLKA--------------PNLVKCPNCGEPK---------LPHRVCPSCG-YYK 49 (56)
T ss_dssp --SS-SCHHHHHHHTT-----TTS--T--------------TSEEESSSSSSEE---------STTSBCTTTB-BSS
T ss_pred CCCCcCChhHccchhc-----cccccc--------------cceeeeccCCCEe---------cccEeeCCCC-eEC
Confidence 5667677666666653 121111 1346799999643 3479999999 444
No 8
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=80.62 E-value=1.6 Score=31.76 Aligned_cols=49 Identities=37% Similarity=0.561 Sum_probs=31.4
Q ss_pred CCCCCCCCCCccccccccccccccccCcCCCcCCCCCCCcCCCCCceeccCCCCCCCCcccCCCCCcccchhhhhhh
Q 026433 108 RVPVRARSKLRTRCRRELLNQEAWWGSVHGSVKAAKPVVSKVIIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRF 184 (238)
Q Consensus 108 ~vP~raRSKR~R~~~~~~~~~~~~~~~~~~~~kk~k~~~~~~~~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~y 184 (238)
.+|-+.-|+.+++.++.- |.. .....-.|.+||...-| +.+|..||.|-
T Consensus 2 AvPKrk~S~srr~~RRsh-----~~l--------------~~~~l~~C~~CG~~~~~---------H~vC~~CG~Y~ 50 (57)
T PRK12286 2 AVPKRKTSKSRKRKRRAH-----FKL--------------KAPGLVECPNCGEPKLP---------HRVCPSCGYYK 50 (57)
T ss_pred CcCcCcCChhhcchhccc-----ccc--------------cCCcceECCCCCCccCC---------eEECCCCCcCC
Confidence 467777776666665531 100 12234579999987655 89999999543
No 9
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=73.72 E-value=0.96 Score=29.90 Aligned_cols=30 Identities=27% Similarity=0.684 Sum_probs=16.5
Q ss_pred ceeccCCCCCCCCcccCCCCCcccchhhhh
Q 026433 153 RKCQHCGAEKTPQWRAGPMGPKTLCNACGV 182 (238)
Q Consensus 153 r~C~nCgtt~TP~WRrGP~G~~~LCNACGL 182 (238)
+.|.+||..-+-.--.|.+-.+..|.+||-
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 369999987544344677778899999984
No 10
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=70.52 E-value=3.1 Score=41.79 Aligned_cols=35 Identities=29% Similarity=0.456 Sum_probs=29.8
Q ss_pred CceeccCCC-CCCCCcccCCCCCcccchhhhhhhhc
Q 026433 152 GRKCQHCGA-EKTPQWRAGPMGPKTLCNACGVRFKS 186 (238)
Q Consensus 152 ~r~C~nCgt-t~TP~WRrGP~G~~~LCNACGL~ykk 186 (238)
...|.+|++ +.||.||+...-.-++|||||+..+.
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~ 332 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKP 332 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCC
Confidence 456788877 78999999888779999999999887
No 11
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=64.05 E-value=2.4 Score=35.71 Aligned_cols=31 Identities=29% Similarity=0.542 Sum_probs=23.6
Q ss_pred ceeccCCCCCCCCcccCCCCCcccchhhhhhh
Q 026433 153 RKCQHCGAEKTPQWRAGPMGPKTLCNACGVRF 184 (238)
Q Consensus 153 r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~y 184 (238)
-.|..|+..+|-+=+++- ---.-|+|||-..
T Consensus 103 VlC~~C~spdT~l~k~~r-~~~l~C~ACGa~~ 133 (138)
T PRK03988 103 VICPECGSPDTKLIKEGR-IWVLKCEACGAET 133 (138)
T ss_pred EECCCCCCCCcEEEEcCC-eEEEEcccCCCCC
Confidence 479999999999977532 2246899999653
No 12
>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=62.85 E-value=6.9 Score=28.16 Aligned_cols=23 Identities=35% Similarity=0.829 Sum_probs=17.2
Q ss_pred CceeccCCCCCCCCcccCCCCCcccchhhhhh
Q 026433 152 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVR 183 (238)
Q Consensus 152 ~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ 183 (238)
.-.|.+||...- ++.+|-.||.|
T Consensus 26 l~~C~~cG~~~~---------~H~vc~~cG~Y 48 (55)
T TIGR01031 26 LVVCPNCGEFKL---------PHRVCPSCGYY 48 (55)
T ss_pred ceECCCCCCccc---------CeeECCccCeE
Confidence 456999997543 47899999933
No 13
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=61.93 E-value=2.6 Score=35.28 Aligned_cols=31 Identities=26% Similarity=0.559 Sum_probs=23.3
Q ss_pred ceeccCCCCCCCCcccCCCCCcccchhhhhhh
Q 026433 153 RKCQHCGAEKTPQWRAGPMGPKTLCNACGVRF 184 (238)
Q Consensus 153 r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~y 184 (238)
-.|..|+..+|-+=+.+. ---.-|+|||-..
T Consensus 98 VlC~~C~sPdT~l~k~~r-~~~l~C~ACGa~~ 128 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGR-VSLLKCEACGAKA 128 (133)
T ss_pred EECCCCCCCCcEEEEeCC-eEEEecccCCCCC
Confidence 479999999999887532 2135899999653
No 14
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=59.82 E-value=3.1 Score=33.71 Aligned_cols=29 Identities=28% Similarity=0.592 Sum_probs=22.2
Q ss_pred ceeccCCCCCCCCcccCCCCCcccchhhhh
Q 026433 153 RKCQHCGAEKTPQWRAGPMGPKTLCNACGV 182 (238)
Q Consensus 153 r~C~nCgtt~TP~WRrGP~G~~~LCNACGL 182 (238)
-.|..|+..+|-+=+.+..= -.-|+|||-
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 47999999999998872211 356999995
No 15
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=56.52 E-value=3.8 Score=36.07 Aligned_cols=32 Identities=25% Similarity=0.468 Sum_probs=24.6
Q ss_pred ceeccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 026433 153 RKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 185 (238)
Q Consensus 153 r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~yk 185 (238)
-.|..|+..+|-+=+.+. ---.-|+|||-..-
T Consensus 99 V~C~~C~~pdT~l~k~~~-~~~l~C~aCGa~~~ 130 (201)
T PRK12336 99 VICSECGLPDTRLVKEDR-VLMLRCDACGAHRP 130 (201)
T ss_pred EECCCCCCCCcEEEEcCC-eEEEEcccCCCCcc
Confidence 479999999999987632 11358999998764
No 16
>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=52.22 E-value=4.5 Score=27.03 Aligned_cols=30 Identities=27% Similarity=0.727 Sum_probs=19.2
Q ss_pred eeccCCCCCCCCcccCCCCCcccchhhhhhhhc
Q 026433 154 KCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKS 186 (238)
Q Consensus 154 ~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ykk 186 (238)
.|.+|+... .--....| ...|..||+-..-
T Consensus 2 ~Cp~Cg~~~--~~~D~~~g-~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKE--IVFDPERG-ELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSE--EEEETTTT-EEEETTT-BBEE-
T ss_pred CCcCCcCCc--eEEcCCCC-eEECCCCCCEeec
Confidence 689999866 22223345 7899999987654
No 17
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=51.43 E-value=10 Score=27.75 Aligned_cols=48 Identities=25% Similarity=0.250 Sum_probs=29.6
Q ss_pred CCCCCCCCCCccccccccccccccccCcCCCcCCCCCCCcCCCCCceeccCCCCCCCCcccCCCCCcccchhhhhhh
Q 026433 108 RVPVRARSKLRTRCRRELLNQEAWWGSVHGSVKAAKPVVSKVIIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRF 184 (238)
Q Consensus 108 ~vP~raRSKR~R~~~~~~~~~~~~~~~~~~~~kk~k~~~~~~~~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~y 184 (238)
.||-+.-||.+++.++.. |... ......|.+||...-| +.+|- ||.|.
T Consensus 2 AVPKrK~Sksr~~~RRa~-----~~~~--------------~~~~~~c~~cg~~~~p---------H~vc~-cG~Y~ 49 (60)
T PRK01110 2 AVPKRKTSKSKRRMRRSH-----WKLT--------------APTLSVDKTTGEYHLP---------HHVSP-KGYYK 49 (60)
T ss_pred CCCcCccchhhchhhhhh-----hhcc--------------CCceeEcCCCCceecc---------ceecC-CcccC
Confidence 467777777777666531 2111 1224679999986544 67899 99554
No 18
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=50.07 E-value=11 Score=30.29 Aligned_cols=35 Identities=17% Similarity=0.300 Sum_probs=23.2
Q ss_pred CCceeccCCCCCCCCcccCCCCCcccchhhhhhhhc
Q 026433 151 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKS 186 (238)
Q Consensus 151 ~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ykk 186 (238)
..-.|.+|+.. +-.-..+-...+..|-.||.++..
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 34679999953 222222224558999999999865
No 19
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=49.21 E-value=7.8 Score=36.82 Aligned_cols=35 Identities=34% Similarity=0.787 Sum_probs=29.8
Q ss_pred CCCceeccCCCCCCCCcccCCCCCcccchhhhhhhhc
Q 026433 150 IIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKS 186 (238)
Q Consensus 150 ~~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ykk 186 (238)
...+.|+.|++.. |+|-.=.-| -.||--|.=-.+.
T Consensus 18 ~~Nk~CaDCga~~-P~W~S~nlG-vfiCi~CagvHRs 52 (319)
T COG5347 18 SSNKKCADCGAPN-PTWASVNLG-VFLCIDCAGVHRS 52 (319)
T ss_pred cccCccccCCCCC-CceEecccC-eEEEeecchhhhc
Confidence 4467899999999 999999999 9999999755543
No 20
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=48.75 E-value=9 Score=27.34 Aligned_cols=34 Identities=21% Similarity=0.590 Sum_probs=25.0
Q ss_pred CCCCCceeccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 026433 148 KVIIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 185 (238)
Q Consensus 148 ~~~~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~yk 185 (238)
+......|..||...-- ...+....|..||..+.
T Consensus 24 ~~~TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 24 EAYTSQTCPRCGHRNKK----RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CCCCccCccCccccccc----ccccceEEcCCCCCEEC
Confidence 34456789999987654 45666789999998764
No 21
>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=48.45 E-value=9.7 Score=32.81 Aligned_cols=34 Identities=26% Similarity=0.515 Sum_probs=26.6
Q ss_pred ceeccCCCCCCCCc--ccCCCC----Ccccchhhhhhhhc
Q 026433 153 RKCQHCGAEKTPQW--RAGPMG----PKTLCNACGVRFKS 186 (238)
Q Consensus 153 r~C~nCgtt~TP~W--RrGP~G----~~~LCNACGL~ykk 186 (238)
+.|..|+..+|-.- |...+| .+-.|.+||-+|-.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTT 40 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTT 40 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccce
Confidence 57999999998886 555566 34789999999854
No 22
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=47.73 E-value=23 Score=25.92 Aligned_cols=49 Identities=35% Similarity=0.676 Sum_probs=32.7
Q ss_pred CceeccCCCCCCCCcccCCCCCcccchhhhhhhhcCCCCCCCCCCCCCCCCcccccchhHHHHHHHHh
Q 026433 152 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKSGRLVPEYRPANSPTFSSELHSNSHRKVVEMRRQ 219 (238)
Q Consensus 152 ~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ykk~rllp~yrpa~sPtf~~~~hsn~hrkv~~~R~q 219 (238)
.+.|..||+..- +..|-.||.... .+--|.|++.-.-..+|-.++.|..
T Consensus 5 mr~C~~CgvYTL----------k~~CP~CG~~t~---------~~~P~rfSp~D~y~~yR~~~kk~~~ 53 (56)
T PRK13130 5 IRKCPKCGVYTL----------KEICPVCGGKTK---------NPHPPRFSPEDKYGKYRRALKKRRK 53 (56)
T ss_pred ceECCCCCCEEc----------cccCcCCCCCCC---------CCCCCCCCCCCccHHHHHHHHHHhh
Confidence 467888887654 457777886643 3445677777667778777776654
No 23
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.34 E-value=10 Score=39.61 Aligned_cols=45 Identities=18% Similarity=0.431 Sum_probs=34.1
Q ss_pred CcCCCCCceeccCCCCCCCCcccCCCC---CcccchhhhhhhhcCCCC
Q 026433 146 VSKVIIGRKCQHCGAEKTPQWRAGPMG---PKTLCNACGVRFKSGRLV 190 (238)
Q Consensus 146 ~~~~~~~r~C~nCgtt~TP~WRrGP~G---~~~LCNACGL~ykk~rll 190 (238)
.......-.|..|.+.-||.|+.-+.+ .+.+|.+|-.--.|+.+-
T Consensus 456 t~~a~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSnqkkAlK 503 (706)
T KOG3740|consen 456 TTLATEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSNQKKALK 503 (706)
T ss_pred ccccCCchhhhhcccccccccccccccCcchHHHHHhhhhhccccccc
Confidence 334555778999999999999887766 468999998766554443
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=45.78 E-value=6.2 Score=32.65 Aligned_cols=29 Identities=31% Similarity=0.670 Sum_probs=23.3
Q ss_pred ceeccCCCCCCCCcccCCCCCcccchhhhh
Q 026433 153 RKCQHCGAEKTPQWRAGPMGPKTLCNACGV 182 (238)
Q Consensus 153 r~C~nCgtt~TP~WRrGP~G~~~LCNACGL 182 (238)
-.|..|+..+|-+=+++..= -.-|+|||-
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 36999999999998874433 578999995
No 25
>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=44.56 E-value=10 Score=26.03 Aligned_cols=26 Identities=38% Similarity=0.928 Sum_probs=20.0
Q ss_pred CCceeccCCCCCCCCcccCCCCCcccchhhh
Q 026433 151 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACG 181 (238)
Q Consensus 151 ~~r~C~nCgtt~TP~WRrGP~G~~~LCNACG 181 (238)
....|..| .+|+.| ..+| +..|-+|+
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 35578889 589999 3466 78999996
No 26
>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=41.26 E-value=16 Score=29.07 Aligned_cols=35 Identities=31% Similarity=0.662 Sum_probs=24.8
Q ss_pred CCCceeccCCCCCCCCcccCCCCCcccchhhhhhhhc
Q 026433 150 IIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKS 186 (238)
Q Consensus 150 ~~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ykk 186 (238)
...+.|++|+... |.|-.=..| -.||-.|.-..+.
T Consensus 11 ~~N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~ 45 (116)
T PF01412_consen 11 PGNKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRS 45 (116)
T ss_dssp TTCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHH
T ss_pred cCcCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHH
Confidence 3467899999655 699998899 8999999988776
No 27
>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=38.40 E-value=17 Score=28.80 Aligned_cols=33 Identities=36% Similarity=0.841 Sum_probs=28.5
Q ss_pred CceeccCCCCCCCCcccCCCCCcccchhhhhhhhc
Q 026433 152 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKS 186 (238)
Q Consensus 152 ~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ykk 186 (238)
.+.|++|+. .-|.|-.=..| -.+|-.|.-..+.
T Consensus 3 N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~ 35 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRS 35 (112)
T ss_pred CCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHh
Confidence 578999998 45999988889 8999999887775
No 28
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=37.45 E-value=18 Score=35.57 Aligned_cols=35 Identities=29% Similarity=0.661 Sum_probs=29.2
Q ss_pred CCCceeccCCCCCCCCcccCCCCCcccchhhhhhhhc
Q 026433 150 IIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKS 186 (238)
Q Consensus 150 ~~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ykk 186 (238)
..++.|+.|+... |.|-.=..| -.||-.|.=..+.
T Consensus 20 PgNk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRs 54 (395)
T PLN03114 20 SDNKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRS 54 (395)
T ss_pred cCCCcCccCCCCC-CCceeeccc-eeehhhhhHhhcc
Confidence 3567899999875 999999999 8999999766654
No 29
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=37.16 E-value=16 Score=34.30 Aligned_cols=30 Identities=30% Similarity=0.671 Sum_probs=24.4
Q ss_pred CceeccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 026433 152 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 185 (238)
Q Consensus 152 ~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~yk 185 (238)
.+.|..||+...+. ..|.+..|+.||..+.
T Consensus 111 ~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~f 140 (279)
T COG2816 111 HRFCGRCGTKTYPR----EGGWARVCPKCGHEHF 140 (279)
T ss_pred CcCCCCCCCcCccc----cCceeeeCCCCCCccC
Confidence 57899999988763 4566899999998874
No 30
>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=35.57 E-value=17 Score=24.18 Aligned_cols=32 Identities=28% Similarity=0.621 Sum_probs=21.5
Q ss_pred CceeccCCCCCCCCcccCCCCCcccchhhhhh
Q 026433 152 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVR 183 (238)
Q Consensus 152 ~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ 183 (238)
..+|.+|++---|.-.-...|....||-|+..
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 35799999999998888888888999999974
No 31
>PRK00420 hypothetical protein; Validated
Probab=35.05 E-value=19 Score=29.58 Aligned_cols=31 Identities=23% Similarity=0.664 Sum_probs=24.1
Q ss_pred CCceeccCCCCCCCCcccCCCCCcccchhhhhhhhc
Q 026433 151 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKS 186 (238)
Q Consensus 151 ~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ykk 186 (238)
....|..|| +|+.|- .+| +..|-+||..+..
T Consensus 22 l~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 22 LSKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred ccCCCCCCC---Ccceec-CCC-ceECCCCCCeeee
Confidence 446798898 688874 456 8999999998764
No 32
>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=32.88 E-value=9.1 Score=25.49 Aligned_cols=32 Identities=28% Similarity=0.733 Sum_probs=19.1
Q ss_pred eeccCCCCCCCCc----ccCCCCCc--ccchhhhhhhh
Q 026433 154 KCQHCGAEKTPQW----RAGPMGPK--TLCNACGVRFK 185 (238)
Q Consensus 154 ~C~nCgtt~TP~W----RrGP~G~~--~LCNACGL~yk 185 (238)
.|..|+..++--| |.++++.- ..|..||-+|+
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 4888888764433 55655522 57999998774
No 33
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=32.45 E-value=9.1 Score=29.00 Aligned_cols=35 Identities=23% Similarity=0.413 Sum_probs=26.7
Q ss_pred CCceeccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 026433 151 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 185 (238)
Q Consensus 151 ~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~yk 185 (238)
.+-.|.-|.+.+|=+|.+-..-...-|-+||-..+
T Consensus 9 AGA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~ 43 (66)
T COG3529 9 AGAVCPACQAQDTLAMWRENNVEIVECVKCGHHMR 43 (66)
T ss_pred ccCCCcccchhhHHHHHHhcCCceEehhhcchHhh
Confidence 34579999999997755544455889999998764
No 34
>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=31.91 E-value=14 Score=27.93 Aligned_cols=36 Identities=22% Similarity=0.314 Sum_probs=28.3
Q ss_pred CCceeccCCCCCCCCcccCCCCCcccchhhhhhhhc
Q 026433 151 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKS 186 (238)
Q Consensus 151 ~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ykk 186 (238)
.+-.|-.|...+|=+|.+..+-...-|-+||-.-..
T Consensus 7 AGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~ 42 (71)
T PF09526_consen 7 AGAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQ 42 (71)
T ss_pred cCccCCCCcCccEEEEEEeCCceEEEecCCCCeecc
Confidence 356799999999988665555668899999987654
No 35
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=31.31 E-value=10 Score=23.90 Aligned_cols=29 Identities=38% Similarity=0.801 Sum_probs=16.2
Q ss_pred CceeccCCCCCCCCcccCCCCCcccchhhhhhh
Q 026433 152 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRF 184 (238)
Q Consensus 152 ~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~y 184 (238)
.+.|..||....+. +.|....|.+||..+
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 36799999876543 346678899998754
No 36
>PRK04023 DNA polymerase II large subunit; Validated
Probab=31.21 E-value=22 Score=39.08 Aligned_cols=20 Identities=25% Similarity=0.315 Sum_probs=16.0
Q ss_pred hccccccccccccccccCCC
Q 026433 219 QKQMMGIELGVLGVKPVDKG 238 (238)
Q Consensus 219 qk~~~~~~~g~~~~~~~~~~ 238 (238)
-|++.|++++.-+..|++||
T Consensus 703 ~KGVkgl~S~~k~~EPlEKG 722 (1121)
T PRK04023 703 VKGVKGLTSKDKIPEPLEKG 722 (1121)
T ss_pred cccceecccCCCCCcchHhh
Confidence 36777888888888888887
No 37
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=31.09 E-value=27 Score=35.22 Aligned_cols=49 Identities=31% Similarity=0.642 Sum_probs=32.5
Q ss_pred ceeccCCCCC-CCCcccCCCCCc----------ccchhhhhhhhcCCCCCCCCCCCCCCCCcccccchhHHHHHHHHh
Q 026433 153 RKCQHCGAEK-TPQWRAGPMGPK----------TLCNACGVRFKSGRLVPEYRPANSPTFSSELHSNSHRKVVEMRRQ 219 (238)
Q Consensus 153 r~C~nCgtt~-TP~WRrGP~G~~----------~LCNACGL~ykk~rllp~yrpa~sPtf~~~~hsn~hrkv~~~R~q 219 (238)
-.|.+||... +++=+-+|.+.. +.||+||---+ .|+| |...|+++.|+-
T Consensus 162 PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~R----FPRY--------------Ndp~kLLeTRkG 221 (500)
T KOG0909|consen 162 PPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETR----FPRY--------------NDPIKLLETRKG 221 (500)
T ss_pred CCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCccc----Cccc--------------CCHHHHHhhccC
Confidence 4699999877 555454554432 78999997654 3444 456677777753
No 38
>PF12773 DZR: Double zinc ribbon
Probab=29.54 E-value=39 Score=22.64 Aligned_cols=30 Identities=30% Similarity=0.703 Sum_probs=20.4
Q ss_pred CCceeccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 026433 151 IGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 185 (238)
Q Consensus 151 ~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~yk 185 (238)
..+.|.+||+.-. .+......|..||-...
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGAENP 40 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcCCCc
Confidence 3567888888766 33444678888887644
No 39
>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=29.21 E-value=28 Score=23.56 Aligned_cols=27 Identities=30% Similarity=0.624 Sum_probs=19.3
Q ss_pred ceeccCCCCCCCCcccCCCCCcccchhhhh
Q 026433 153 RKCQHCGAEKTPQWRAGPMGPKTLCNACGV 182 (238)
Q Consensus 153 r~C~nCgtt~TP~WRrGP~G~~~LCNACGL 182 (238)
..|.+||.+ ..-|-++ .+ ..-|++|+-
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 469999998 4545444 34 789999974
No 40
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=28.50 E-value=34 Score=20.75 Aligned_cols=23 Identities=39% Similarity=1.015 Sum_probs=14.5
Q ss_pred ceeccCCCCCCCCcccCCCCCcccchhhhhh
Q 026433 153 RKCQHCGAEKTPQWRAGPMGPKTLCNACGVR 183 (238)
Q Consensus 153 r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ 183 (238)
+.|.+||....+ + ...|-.||..
T Consensus 3 ~~Cp~Cg~~~~~-------~-~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDP-------D-AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCc-------c-cccChhhCCC
Confidence 568888875422 2 4567777753
No 41
>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=28.49 E-value=38 Score=22.79 Aligned_cols=29 Identities=24% Similarity=0.715 Sum_probs=21.0
Q ss_pred ceeccCCCCCCCCcccC-CCCCcccchhhhh
Q 026433 153 RKCQHCGAEKTPQWRAG-PMGPKTLCNACGV 182 (238)
Q Consensus 153 r~C~nCgtt~TP~WRrG-P~G~~~LCNACGL 182 (238)
..|..|+..+.=.|... ..| ...|+.||.
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 46999998887767553 234 789999974
No 42
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=28.19 E-value=30 Score=29.69 Aligned_cols=34 Identities=32% Similarity=0.687 Sum_probs=22.8
Q ss_pred ceeccCCCCCCCCcccC--CCC----Ccccchhhhhhhhc
Q 026433 153 RKCQHCGAEKTPQWRAG--PMG----PKTLCNACGVRFKS 186 (238)
Q Consensus 153 r~C~nCgtt~TP~WRrG--P~G----~~~LCNACGL~ykk 186 (238)
+.|.+||...|-.--.. +.| ...-|.+||-.|..
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~ 40 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT 40 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence 46999999887664221 123 23789999998853
No 43
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=27.68 E-value=33 Score=34.96 Aligned_cols=31 Identities=29% Similarity=0.747 Sum_probs=21.7
Q ss_pred ceeccCCCCCCCCcccCCCCCcccchhhhhhhhc
Q 026433 153 RKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFKS 186 (238)
Q Consensus 153 r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ykk 186 (238)
+.|.||+.+. +. |+-.+| ...|.|||.-..-
T Consensus 1 ~~C~~C~~s~-fe-~d~a~g-~~~C~~CG~v~E~ 31 (521)
T KOG1598|consen 1 MVCKNCGGSN-FE-RDEATG-NLYCTACGTVLEY 31 (521)
T ss_pred CcCCCCCCCC-cc-cccccC-Cceeccccceeec
Confidence 4699999864 22 222455 8999999987754
No 44
>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=27.51 E-value=57 Score=24.70 Aligned_cols=43 Identities=16% Similarity=0.390 Sum_probs=32.1
Q ss_pred CCceeccCCCCCCCCc---ccCCCCCcccchhhhhhhhcCCCCCCC
Q 026433 151 IGRKCQHCGAEKTPQW---RAGPMGPKTLCNACGVRFKSGRLVPEY 193 (238)
Q Consensus 151 ~~r~C~nCgtt~TP~W---RrGP~G~~~LCNACGL~ykk~rllp~y 193 (238)
....|..|..++|--= --...-|+..|-+|..+|..|+.+...
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 4567999999888652 223345689999999999998876544
No 45
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=26.56 E-value=40 Score=31.19 Aligned_cols=11 Identities=27% Similarity=0.510 Sum_probs=5.7
Q ss_pred CCCceeccCCC
Q 026433 150 IIGRKCQHCGA 160 (238)
Q Consensus 150 ~~~r~C~nCgt 160 (238)
.....|.+||.
T Consensus 28 ~Ge~vC~~CG~ 38 (310)
T PRK00423 28 RGEIVCADCGL 38 (310)
T ss_pred CCeEeecccCC
Confidence 34455555554
No 46
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=26.41 E-value=28 Score=31.53 Aligned_cols=30 Identities=30% Similarity=0.593 Sum_probs=22.2
Q ss_pred CceeccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 026433 152 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 185 (238)
Q Consensus 152 ~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~yk 185 (238)
.+.|..||...... ..|....|.+||..+-
T Consensus 99 ~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 99 HRFCGYCGHPMHPS----KTEWAMLCPHCRERYY 128 (256)
T ss_pred CccccccCCCCeec----CCceeEECCCCCCEEC
Confidence 46899999975542 4566788999997653
No 47
>PF14122 YokU: YokU-like protein
Probab=26.27 E-value=25 Score=28.06 Aligned_cols=34 Identities=29% Similarity=0.861 Sum_probs=22.6
Q ss_pred eeccCCCCC-----CCCcccCCCCC---------cccchhhhhhhhcC
Q 026433 154 KCQHCGAEK-----TPQWRAGPMGP---------KTLCNACGVRFKSG 187 (238)
Q Consensus 154 ~C~nCgtt~-----TP~WRrGP~G~---------~~LCNACGL~ykk~ 187 (238)
.|..|+..+ +.....=|+|. ...|+.||+-|...
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~d 48 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQDD 48 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEehh
Confidence 388888753 33333445554 47899999999753
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=25.49 E-value=30 Score=22.95 Aligned_cols=25 Identities=32% Similarity=0.864 Sum_probs=19.6
Q ss_pred ceeccCCCCCCCCcccCCCCCcccchhhhh
Q 026433 153 RKCQHCGAEKTPQWRAGPMGPKTLCNACGV 182 (238)
Q Consensus 153 r~C~nCgtt~TP~WRrGP~G~~~LCNACGL 182 (238)
..|..|+.. |-...+| ...|..||-
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 6666678 889999985
No 49
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=25.17 E-value=26 Score=22.99 Aligned_cols=31 Identities=32% Similarity=0.747 Sum_probs=23.7
Q ss_pred eeccCCCC-CCCCcccCCCCCcccchhhhhhh
Q 026433 154 KCQHCGAE-KTPQWRAGPMGPKTLCNACGVRF 184 (238)
Q Consensus 154 ~C~nCgtt-~TP~WRrGP~G~~~LCNACGL~y 184 (238)
.|.+|++. .-+..+-.+.|...-|-.||-.|
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 68888875 46667777888888888888655
No 50
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=24.13 E-value=44 Score=24.61 Aligned_cols=23 Identities=35% Similarity=0.820 Sum_probs=15.3
Q ss_pred CceeccCCCCCCCCcccCCCCCcccchhhhhh
Q 026433 152 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGVR 183 (238)
Q Consensus 152 ~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~ 183 (238)
.-.|.+||...=| +.+|-.||.+
T Consensus 27 ~~~c~~cG~~~l~---------Hrvc~~cg~Y 49 (57)
T COG0333 27 LSVCPNCGEYKLP---------HRVCLKCGYY 49 (57)
T ss_pred ceeccCCCCcccC---------ceEcCCCCCc
Confidence 3568888865432 6778888843
No 51
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=23.60 E-value=51 Score=22.04 Aligned_cols=30 Identities=27% Similarity=0.660 Sum_probs=19.4
Q ss_pred eeccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 026433 154 KCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 185 (238)
Q Consensus 154 ~C~nCgtt~TP~WRrGP~G~~~LCNACGL~yk 185 (238)
.|..||..-.+. .+.......|..||-.+.
T Consensus 2 FCp~Cg~~l~~~--~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNMLIPK--EGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCccccc--cCCCCCEEECCcCCCeEE
Confidence 589999855443 111223789999996654
No 52
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=23.36 E-value=41 Score=31.63 Aligned_cols=36 Identities=28% Similarity=0.540 Sum_probs=25.4
Q ss_pred CCCCceeccCCCCCCCCc----ccCCCCCc---ccchhhhhhhh
Q 026433 149 VIIGRKCQHCGAEKTPQW----RAGPMGPK---TLCNACGVRFK 185 (238)
Q Consensus 149 ~~~~r~C~nCgtt~TP~W----RrGP~G~~---~LCNACGL~yk 185 (238)
.+....|..|+-...--| |...++ - ..|..||-+|+
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 344578999998776555 433333 3 48999999986
No 53
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=22.81 E-value=41 Score=29.15 Aligned_cols=29 Identities=28% Similarity=0.698 Sum_probs=23.9
Q ss_pred CceeccCCCCCCCCcccCCCCCcccchhhh
Q 026433 152 GRKCQHCGAEKTPQWRAGPMGPKTLCNACG 181 (238)
Q Consensus 152 ~r~C~nCgtt~TP~WRrGP~G~~~LCNACG 181 (238)
...|..||......|-.-.+| ..+|..|+
T Consensus 149 l~~C~~Cg~~~~~~~f~~~~g-g~~c~~c~ 177 (247)
T PRK00085 149 LDHCAVCGAPGDHRYFSPKEG-GAVCSECG 177 (247)
T ss_pred hhhHhcCCCCCCceEEecccC-Cccccccc
Confidence 357999998877677777777 89999997
No 54
>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=22.80 E-value=43 Score=29.33 Aligned_cols=34 Identities=26% Similarity=0.489 Sum_probs=25.5
Q ss_pred ceeccCCCCCCCCcccCCCCCc--ccchhhhhhhhc
Q 026433 153 RKCQHCGAEKTPQWRAGPMGPK--TLCNACGVRFKS 186 (238)
Q Consensus 153 r~C~nCgtt~TP~WRrGP~G~~--~LCNACGL~ykk 186 (238)
++|.+||..-..++|+=..|.- +-|..||..-.|
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaDk 36 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVADK 36 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCcccc
Confidence 4799999998888888443322 789999976544
No 55
>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=22.79 E-value=44 Score=29.27 Aligned_cols=32 Identities=19% Similarity=0.676 Sum_probs=23.4
Q ss_pred ceeccCCCCCCCCccc-------CCCCCcccchhhhhhh
Q 026433 153 RKCQHCGAEKTPQWRA-------GPMGPKTLCNACGVRF 184 (238)
Q Consensus 153 r~C~nCgtt~TP~WRr-------GP~G~~~LCNACGL~y 184 (238)
..|.+|++..--.|-- ++.-...-|+.||..|
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 5689998876555532 4455568899999998
No 56
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=22.40 E-value=47 Score=29.05 Aligned_cols=34 Identities=38% Similarity=0.775 Sum_probs=26.4
Q ss_pred ceeccCCCCCCCCc--ccCCCCC----cccchhhhhhhhc
Q 026433 153 RKCQHCGAEKTPQW--RAGPMGP----KTLCNACGVRFKS 186 (238)
Q Consensus 153 r~C~nCgtt~TP~W--RrGP~G~----~~LCNACGL~ykk 186 (238)
+.|..|+..+|..- |.-.+|. +--|..||-+|-.
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTT 40 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTT 40 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhcccccccccch
Confidence 46999999999886 6666663 3689999999853
No 57
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.26 E-value=49 Score=28.65 Aligned_cols=29 Identities=24% Similarity=0.572 Sum_probs=22.9
Q ss_pred CCCCCceeccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 026433 148 KVIIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 185 (238)
Q Consensus 148 ~~~~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~yk 185 (238)
.......|..||. ..+....|..||..+.
T Consensus 305 ~~~tS~~C~~cg~---------~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 305 PYYTSKTCPCCGH---------LSGRLFKCPRCGFVHD 333 (364)
T ss_pred CCCCcccccccCC---------ccceeEECCCCCCeeh
Confidence 4566789999999 4465789999998764
No 58
>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=22.24 E-value=33 Score=22.97 Aligned_cols=28 Identities=25% Similarity=0.605 Sum_probs=17.4
Q ss_pred eeccCCCCCCCCcccCCCCCcccchhhhh
Q 026433 154 KCQHCGAEKTPQWRAGPMGPKTLCNACGV 182 (238)
Q Consensus 154 ~C~nCgtt~TP~WRrGP~G~~~LCNACGL 182 (238)
+|..||..-+-...-.. .....|-+||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 57888865544433333 44678888886
No 59
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=21.97 E-value=38 Score=32.12 Aligned_cols=29 Identities=31% Similarity=0.890 Sum_probs=25.2
Q ss_pred CceeccCCCCCCCCcccCCCCCcccchhhhh
Q 026433 152 GRKCQHCGAEKTPQWRAGPMGPKTLCNACGV 182 (238)
Q Consensus 152 ~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL 182 (238)
.+.|+.|++. .|.|-.=--| -.+|=.|-=
T Consensus 25 N~~CADC~a~-~P~WaSwnlG-vFiC~~C~g 53 (287)
T KOG0703|consen 25 NKVCADCGAK-GPRWASWNLG-VFICLRCAG 53 (287)
T ss_pred cCcccccCCC-CCCeEEeecC-eEEEeeccc
Confidence 6889999999 9999987888 889988743
No 60
>COG3952 Predicted membrane protein [Function unknown]
Probab=21.74 E-value=22 Score=29.51 Aligned_cols=18 Identities=33% Similarity=0.514 Sum_probs=13.9
Q ss_pred cccCCCCCcccchhhhhhhh
Q 026433 166 WRAGPMGPKTLCNACGVRFK 185 (238)
Q Consensus 166 WRrGP~G~~~LCNACGL~yk 185 (238)
||.+|-+ .||+|||++-.
T Consensus 77 ~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 77 RRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HhcchHH--HHHHhhhHHHH
Confidence 5666655 89999999864
No 61
>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=21.11 E-value=46 Score=33.47 Aligned_cols=35 Identities=29% Similarity=0.812 Sum_probs=27.8
Q ss_pred CCceeccCCCCCCCCccc-------CCCCCcccchhhhhhhh
Q 026433 151 IGRKCQHCGAEKTPQWRA-------GPMGPKTLCNACGVRFK 185 (238)
Q Consensus 151 ~~r~C~nCgtt~TP~WRr-------GP~G~~~LCNACGL~yk 185 (238)
--..|-|||......|.. .|....+.|-.||-.+.
T Consensus 199 ~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred EEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCC
Confidence 346899999999998743 25556799999998885
No 62
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=20.96 E-value=74 Score=25.81 Aligned_cols=15 Identities=40% Similarity=1.081 Sum_probs=10.1
Q ss_pred CCCcccchhhhhhhh
Q 026433 171 MGPKTLCNACGVRFK 185 (238)
Q Consensus 171 ~G~~~LCNACGL~yk 185 (238)
-|.|.+|..||.+|-
T Consensus 6 lGtKR~Cp~CG~kFY 20 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFY 20 (108)
T ss_pred cCCcccCCCCcchhc
Confidence 356777777777664
No 63
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=20.71 E-value=54 Score=34.23 Aligned_cols=35 Identities=23% Similarity=0.515 Sum_probs=27.9
Q ss_pred CCCCceeccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 026433 149 VIIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 185 (238)
Q Consensus 149 ~~~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~yk 185 (238)
....+.|++|+... |.|-.=.-| -.+|-.|.=..+
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 34568899999866 999888888 899999965443
No 64
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=20.59 E-value=44 Score=37.62 Aligned_cols=20 Identities=25% Similarity=0.331 Sum_probs=16.6
Q ss_pred hccccccccccccccccCCC
Q 026433 219 QKQMMGIELGVLGVKPVDKG 238 (238)
Q Consensus 219 qk~~~~~~~g~~~~~~~~~~ 238 (238)
-|++.|+.++.-+..|++||
T Consensus 750 ~KgVkgl~S~~k~~EplEKG 769 (1337)
T PRK14714 750 LKGVKGLTSREKIPEPLEKG 769 (1337)
T ss_pred cccceecccCCCCCcchHhh
Confidence 46788888888889998887
No 65
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=20.30 E-value=34 Score=36.95 Aligned_cols=21 Identities=24% Similarity=0.321 Sum_probs=0.0
Q ss_pred HhccccccccccccccccCCC
Q 026433 218 RQKQMMGIELGVLGVKPVDKG 238 (238)
Q Consensus 218 ~qk~~~~~~~g~~~~~~~~~~ 238 (238)
.-|++.|+++..-...|++||
T Consensus 731 ~~KGVkgl~S~~k~pEPlEKG 751 (900)
T PF03833_consen 731 ELKGVKGLTSKEKIPEPLEKG 751 (900)
T ss_dssp ---------------------
T ss_pred hhhhHHhhhccccCcchHHHH
Confidence 346788888888888898887
No 66
>PLN03131 hypothetical protein; Provisional
Probab=20.04 E-value=57 Score=34.37 Aligned_cols=35 Identities=20% Similarity=0.493 Sum_probs=28.0
Q ss_pred CCCCceeccCCCCCCCCcccCCCCCcccchhhhhhhh
Q 026433 149 VIIGRKCQHCGAEKTPQWRAGPMGPKTLCNACGVRFK 185 (238)
Q Consensus 149 ~~~~r~C~nCgtt~TP~WRrGP~G~~~LCNACGL~yk 185 (238)
...++.|++|+... |.|-.=..| -.+|-.|.=..+
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 34578999999865 999988888 899999965543
Done!