Query 019919
Match_columns 334
No_of_seqs 228 out of 736
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 05:34:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019919.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019919hhsearch_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 1.7E-14 3.7E-19 107.4 3.7 44 228-274 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.5 3.1E-14 6.6E-19 105.1 3.6 39 225-263 2-40 (52)
3 PF00320 GATA: GATA zinc finge 99.4 4.1E-14 9E-19 97.3 0.2 35 229-263 1-35 (36)
4 KOG1601 GATA-4/5/6 transcripti 99.2 2.7E-11 5.8E-16 105.0 4.2 71 226-296 199-303 (340)
5 COG5641 GAT1 GATA Zn-finger-co 98.1 1.5E-06 3.2E-11 89.4 2.4 53 226-281 158-215 (498)
6 KOG3554 Histone deacetylase co 88.3 0.43 9.2E-06 50.1 3.4 36 225-260 385-422 (693)
7 COG5641 GAT1 GATA Zn-finger-co 69.1 3.3 7.2E-05 43.6 2.4 35 226-260 297-332 (498)
8 PRK14892 putative transcriptio 58.0 8.5 0.00018 32.5 2.4 34 226-260 21-54 (99)
9 PF01783 Ribosomal_L32p: Ribos 50.0 8.7 0.00019 28.8 1.1 28 225-263 25-52 (56)
10 KOG0909 Peptide:N-glycanase [P 49.7 10 0.00022 39.8 1.9 38 226-267 161-209 (500)
11 PF14803 Nudix_N_2: Nudix N-te 49.4 6 0.00013 27.4 0.2 29 228-256 2-30 (34)
12 KOG3740 Uncharacterized conser 47.1 8.3 0.00018 41.9 0.9 35 225-259 461-498 (706)
13 COG5347 GTPase-activating prot 43.3 11 0.00024 37.6 1.0 31 224-256 18-48 (319)
14 PF01096 TFIIS_C: Transcriptio 43.2 5.8 0.00013 27.7 -0.7 32 228-259 2-39 (39)
15 PRK03988 translation initiatio 42.4 8.4 0.00018 34.1 0.0 31 226-257 102-132 (138)
16 PF04810 zf-Sec23_Sec24: Sec23 42.0 13 0.00028 26.0 0.9 32 226-257 2-33 (40)
17 TIGR00311 aIF-2beta translatio 41.1 9 0.0002 33.7 0.0 32 226-258 97-128 (133)
18 PF13717 zinc_ribbon_4: zinc-r 38.4 12 0.00026 25.9 0.3 32 227-258 3-35 (36)
19 TIGR01385 TFSII transcription 37.3 15 0.00033 36.2 1.0 35 225-259 257-297 (299)
20 smart00653 eIF2B_5 domain pres 36.9 11 0.00025 32.0 0.0 30 226-256 80-109 (110)
21 PRK12286 rpmF 50S ribosomal pr 36.6 17 0.00038 27.7 0.9 23 225-256 26-48 (57)
22 PRK12336 translation initiatio 35.8 12 0.00026 34.6 -0.0 33 226-259 98-130 (201)
23 PHA02998 RNA polymerase subuni 34.4 20 0.00044 33.7 1.2 34 226-259 143-182 (195)
24 PF07282 OrfB_Zn_ribbon: Putat 33.7 18 0.0004 27.1 0.7 30 226-259 28-57 (69)
25 PF08271 TF_Zn_Ribbon: TFIIB z 32.8 15 0.00032 25.8 0.1 31 228-261 2-32 (43)
26 TIGR00244 transcriptional regu 29.9 28 0.00061 31.5 1.3 34 228-261 2-41 (147)
27 smart00105 ArfGap Putative GTP 29.5 32 0.00068 28.7 1.5 33 226-260 3-35 (112)
28 COG2816 NPY1 NTP pyrophosphohy 29.1 28 0.00061 34.4 1.3 30 225-258 110-139 (279)
29 smart00440 ZnF_C2C2 C2C2 Zinc 28.8 21 0.00045 25.1 0.3 32 228-259 2-39 (40)
30 PLN03114 ADP-ribosylation fact 28.8 32 0.00069 35.5 1.6 33 225-259 21-53 (395)
31 PF10083 DUF2321: Uncharacteri 28.6 33 0.00071 31.5 1.5 35 225-259 38-79 (158)
32 TIGR02098 MJ0042_CXXC MJ0042 f 28.0 15 0.00034 24.7 -0.5 33 227-259 3-36 (38)
33 PF01873 eIF-5_eIF-2B: Domain 27.2 19 0.00041 31.3 -0.2 29 227-256 94-122 (125)
34 PF14122 YokU: YokU-like prote 26.8 22 0.00048 29.7 0.1 35 228-262 1-49 (87)
35 PF01412 ArfGap: Putative GTPa 26.1 33 0.00072 28.7 1.0 34 225-260 12-45 (116)
36 COG3952 Predicted membrane pro 25.6 18 0.00039 31.4 -0.7 19 239-259 76-94 (113)
37 PF15396 FAM60A: Protein Famil 25.5 26 0.00056 33.5 0.3 20 248-267 49-68 (213)
38 PRK00420 hypothetical protein; 25.3 36 0.00078 29.4 1.1 29 226-259 23-51 (112)
39 PRK00464 nrdR transcriptional 24.9 37 0.0008 30.6 1.1 33 228-260 2-40 (154)
40 PF12760 Zn_Tnp_IS1595: Transp 24.7 40 0.00086 24.0 1.1 27 227-256 19-45 (46)
41 PF05876 Terminase_GpA: Phage 24.7 38 0.00082 35.8 1.4 34 226-259 200-240 (557)
42 COG3529 Predicted nucleic-acid 23.9 14 0.00031 29.2 -1.4 33 227-259 11-43 (66)
43 PF13248 zf-ribbon_3: zinc-rib 23.8 52 0.0011 21.0 1.4 23 227-257 3-25 (26)
44 PF10080 DUF2318: Predicted me 23.1 25 0.00055 29.7 -0.2 31 226-261 35-65 (102)
45 PRK05978 hypothetical protein; 22.3 51 0.0011 29.7 1.5 34 225-261 32-65 (148)
46 PF11781 RRN7: RNA polymerase 21.4 49 0.0011 23.0 1.0 26 226-256 8-33 (36)
47 PF09297 zf-NADH-PPase: NADH p 21.3 28 0.00061 23.0 -0.3 29 226-258 3-31 (32)
48 smart00778 Prim_Zn_Ribbon Zinc 21.3 70 0.0015 22.6 1.7 30 227-256 4-33 (37)
49 PRK00241 nudC NADH pyrophospha 21.0 42 0.00092 32.0 0.8 30 225-258 98-127 (256)
50 PF06677 Auto_anti-p27: Sjogre 20.6 45 0.00097 24.0 0.6 25 226-255 17-41 (41)
51 COG5349 Uncharacterized protei 20.2 47 0.001 29.5 0.8 33 225-260 20-52 (126)
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=99.49 E-value=1.7e-14 Score=107.41 Aligned_cols=44 Identities=43% Similarity=0.950 Sum_probs=39.2
Q ss_pred cccCCCCCCCCCCCCCCCCCcccchhhhhhhhcCCCCCCCCCCCCCc
Q 019919 228 KCLHCASEKTPQWRTGPMGPKTLCNACGVRYKSGRLVPEYRPAASPT 274 (334)
Q Consensus 228 ~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk~grllp~~rPa~spt 274 (334)
.|+||++++||+||+||.|..+|||||||+|++.+ ..||...+.
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 49999999999999999999999999999999866 567777665
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.47 E-value=3.1e-14 Score=105.06 Aligned_cols=39 Identities=54% Similarity=1.062 Sum_probs=35.7
Q ss_pred CCccccCCCCCCCCCCCCCCCCCcccchhhhhhhhcCCC
Q 019919 225 SVRKCLHCASEKTPQWRTGPMGPKTLCNACGVRYKSGRL 263 (334)
Q Consensus 225 ~~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk~grl 263 (334)
..+.|+||+++.||+||+||.|+++|||||||+|++.+.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 357899999999999999999999999999999998654
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=99.40 E-value=4.1e-14 Score=97.29 Aligned_cols=35 Identities=54% Similarity=1.174 Sum_probs=28.0
Q ss_pred ccCCCCCCCCCCCCCCCCCcccchhhhhhhhcCCC
Q 019919 229 CLHCASEKTPQWRTGPMGPKTLCNACGVRYKSGRL 263 (334)
Q Consensus 229 C~~C~~~~TP~WR~GP~G~ktLCNACGlryk~grl 263 (334)
|.||++++||+||+||.|..+||||||++|++.+.
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 89999999999999999999999999999998653
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=99.15 E-value=2.7e-11 Score=105.00 Aligned_cols=71 Identities=59% Similarity=1.160 Sum_probs=60.9
Q ss_pred CccccCCCCCCCCCCCCCCCCCcccchhhhhhhhcC---CCCCCCCCCCCCc--------------cccccccc------
Q 019919 226 VRKCLHCASEKTPQWRTGPMGPKTLCNACGVRYKSG---RLVPEYRPAASPT--------------FVSAKHSN------ 282 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk~g---rllp~~rPa~spt--------------~~~~~hsn------ 282 (334)
...|.+|+++.||+||++|.|++.+|||||++|+++ +.++.++.+..++ +....|.+
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPRNVSPKGSGAVKGRTFTKSLHSNSAQLLL 278 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCccccccccCccccccccCCCccccccCCCCCcccccchhhhhh
Confidence 589999999999999999999999999999999998 7888888877776 45555555
Q ss_pred -----------CchHHHHHHHHHHh
Q 019919 283 -----------SHRKVMELRRQKEM 296 (334)
Q Consensus 283 -----------sh~kv~~lrrqke~ 296 (334)
.+.++.+++|.++.
T Consensus 279 ~~~~~~~~~~~~~~~~~~~~r~~~~ 303 (340)
T KOG1601|consen 279 APSKSEPPLLSSHQRVAEVRRYRES 303 (340)
T ss_pred hhcccCccccccchHHHHHhhccCc
Confidence 67888888887765
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.08 E-value=1.5e-06 Score=89.38 Aligned_cols=53 Identities=32% Similarity=0.585 Sum_probs=46.4
Q ss_pred CccccCCCCCCCCCCCCCCCC----CcccchhhhhhhhcCCCCCCCC-CCCCCcccccccc
Q 019919 226 VRKCLHCASEKTPQWRTGPMG----PKTLCNACGVRYKSGRLVPEYR-PAASPTFVSAKHS 281 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G----~ktLCNACGlryk~grllp~~r-Pa~spt~~~~~hs 281 (334)
...|.+|.+..||.|||+..+ .-.|||||||+|+ ++...| |...++.+++.|.
T Consensus 158 ~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~k---lhg~~r~P~t~ks~~~ks~~ 215 (498)
T COG5641 158 PHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLK---LHGSPRAPISLKSDSIKSRS 215 (498)
T ss_pred cchhccccccCCccccccccccccCCcccccccccccc---ccCCcCCCcccccccccccc
Confidence 459999999999999999994 3799999999999 555667 9999999998886
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=88.27 E-value=0.43 Score=50.15 Aligned_cols=36 Identities=28% Similarity=0.604 Sum_probs=31.2
Q ss_pred CCccccCCCCCCCCCC--CCCCCCCcccchhhhhhhhc
Q 019919 225 SVRKCLHCASEKTPQW--RTGPMGPKTLCNACGVRYKS 260 (334)
Q Consensus 225 ~~~~C~~C~~~~TP~W--R~GP~G~ktLCNACGlryk~ 260 (334)
+++.|.+|+++..-+| +-+|.-.+.||-.|=++|||
T Consensus 385 ~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKK 422 (693)
T KOG3554|consen 385 DGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKK 422 (693)
T ss_pred CCCcccccccccccceeccCCCCccchhhHHHHHHHHH
Confidence 4789999999999999 55565567899999999998
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=69.08 E-value=3.3 Score=43.58 Aligned_cols=35 Identities=29% Similarity=0.415 Sum_probs=29.7
Q ss_pred CccccCCCC-CCCCCCCCCCCCCcccchhhhhhhhc
Q 019919 226 VRKCLHCAS-EKTPQWRTGPMGPKTLCNACGVRYKS 260 (334)
Q Consensus 226 ~~~C~~C~~-~~TP~WR~GP~G~ktLCNACGlryk~ 260 (334)
...|.+|.+ +.||.||+...-...+|||||...+.
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~ 332 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKP 332 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCC
Confidence 567888887 67899988887778999999999885
No 8
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=57.95 E-value=8.5 Score=32.46 Aligned_cols=34 Identities=15% Similarity=0.280 Sum_probs=22.3
Q ss_pred CccccCCCCCCCCCCCCCCCCCcccchhhhhhhhc
Q 019919 226 VRKCLHCASEKTPQWRTGPMGPKTLCNACGVRYKS 260 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk~ 260 (334)
.-.|.+|+...-+.=+.- .-+...|..||.++..
T Consensus 21 ~f~CP~Cge~~v~v~~~k-~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 21 IFECPRCGKVSISVKIKK-NIAIITCGNCGLYTEF 54 (99)
T ss_pred EeECCCCCCeEeeeecCC-CcceEECCCCCCccCE
Confidence 456999995433322211 3447899999999864
No 9
>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=49.99 E-value=8.7 Score=28.83 Aligned_cols=28 Identities=43% Similarity=1.028 Sum_probs=19.9
Q ss_pred CCccccCCCCCCCCCCCCCCCCCcccchhhhhhhhcCCC
Q 019919 225 SVRKCLHCASEKTPQWRTGPMGPKTLCNACGVRYKSGRL 263 (334)
Q Consensus 225 ~~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk~grl 263 (334)
....|.+||...-| ..+|.+|| +|+ |+.
T Consensus 25 ~l~~c~~cg~~~~~---------H~vc~~cG-~y~-~r~ 52 (56)
T PF01783_consen 25 NLVKCPNCGEPKLP---------HRVCPSCG-YYK-GRQ 52 (56)
T ss_dssp SEEESSSSSSEEST---------TSBCTTTB-BSS-SSS
T ss_pred ceeeeccCCCEecc---------cEeeCCCC-eEC-CEE
Confidence 45689999975443 68999999 444 543
No 10
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=49.66 E-value=10 Score=39.82 Aligned_cols=38 Identities=26% Similarity=0.577 Sum_probs=26.6
Q ss_pred CccccCCCCCC-CCCCCCCCCCCc----------ccchhhhhhhhcCCCCCCC
Q 019919 226 VRKCLHCASEK-TPQWRTGPMGPK----------TLCNACGVRYKSGRLVPEY 267 (334)
Q Consensus 226 ~~~C~~C~~~~-TP~WR~GP~G~k----------tLCNACGlryk~grllp~~ 267 (334)
...|.+||... ++.-+.+|.+.. +.||+||---+ .|+|
T Consensus 161 ~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~R----FPRY 209 (500)
T KOG0909|consen 161 NPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETR----FPRY 209 (500)
T ss_pred CCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCccc----Cccc
Confidence 45799999977 566565665432 68999997554 5666
No 11
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=49.37 E-value=6 Score=27.38 Aligned_cols=29 Identities=24% Similarity=0.580 Sum_probs=14.8
Q ss_pred cccCCCCCCCCCCCCCCCCCcccchhhhh
Q 019919 228 KCLHCASEKTPQWRTGPMGPKTLCNACGV 256 (334)
Q Consensus 228 ~C~~C~~~~TP~WR~GP~G~ktLCNACGl 256 (334)
-|.+||..-+-.=-.|..-.+.+|.+||.
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCC
Confidence 58899987432223555555789999984
No 12
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=47.07 E-value=8.3 Score=41.94 Aligned_cols=35 Identities=20% Similarity=0.610 Sum_probs=29.2
Q ss_pred CCccccCCCCCCCCCCCCCCCC---Ccccchhhhhhhh
Q 019919 225 SVRKCLHCASEKTPQWRTGPMG---PKTLCNACGVRYK 259 (334)
Q Consensus 225 ~~~~C~~C~~~~TP~WR~GP~G---~ktLCNACGlryk 259 (334)
++-.|..|.+.-||.|+.-+.| .+++|.+|----.
T Consensus 461 ~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSnq 498 (706)
T KOG3740|consen 461 EPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSNQ 498 (706)
T ss_pred CchhhhhcccccccccccccccCcchHHHHHhhhhhcc
Confidence 5788999999999999998888 3589999975443
No 13
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=43.31 E-value=11 Score=37.57 Aligned_cols=31 Identities=32% Similarity=0.813 Sum_probs=27.6
Q ss_pred CCCccccCCCCCCCCCCCCCCCCCcccchhhhh
Q 019919 224 DSVRKCLHCASEKTPQWRTGPMGPKTLCNACGV 256 (334)
Q Consensus 224 g~~~~C~~C~~~~TP~WR~GP~G~ktLCNACGl 256 (334)
.....|..|+... |+|=.=..| -.||--|.=
T Consensus 18 ~~Nk~CaDCga~~-P~W~S~nlG-vfiCi~Cag 48 (319)
T COG5347 18 SSNKKCADCGAPN-PTWASVNLG-VFLCIDCAG 48 (319)
T ss_pred cccCccccCCCCC-CceEecccC-eEEEeecch
Confidence 3578999999999 999999999 799999954
No 14
>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=43.21 E-value=5.8 Score=27.75 Aligned_cols=32 Identities=25% Similarity=0.590 Sum_probs=20.8
Q ss_pred cccCCCCCCCCC----CCCCCCCCc--ccchhhhhhhh
Q 019919 228 KCLHCASEKTPQ----WRTGPMGPK--TLCNACGVRYK 259 (334)
Q Consensus 228 ~C~~C~~~~TP~----WR~GP~G~k--tLCNACGlryk 259 (334)
.|..|+..++-. =|.+.++.. ..|..||-+|+
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 588899877443 377777743 48999998874
No 15
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=42.40 E-value=8.4 Score=34.06 Aligned_cols=31 Identities=29% Similarity=0.476 Sum_probs=23.3
Q ss_pred CccccCCCCCCCCCCCCCCCCCcccchhhhhh
Q 019919 226 VRKCLHCASEKTPQWRTGPMGPKTLCNACGVR 257 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlr 257 (334)
-..|..|+...|-.=+.+- ---.-|+|||-.
T Consensus 102 yVlC~~C~spdT~l~k~~r-~~~l~C~ACGa~ 132 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGR-IWVLKCEACGAE 132 (138)
T ss_pred cEECCCCCCCCcEEEEcCC-eEEEEcccCCCC
Confidence 4789999999998876531 113589999964
No 16
>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=42.01 E-value=13 Score=26.04 Aligned_cols=32 Identities=25% Similarity=0.572 Sum_probs=21.2
Q ss_pred CccccCCCCCCCCCCCCCCCCCcccchhhhhh
Q 019919 226 VRKCLHCASEKTPQWRTGPMGPKTLCNACGVR 257 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlr 257 (334)
+.+|.+|++---|.=+-...|..-.||-|+..
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 56899999999888887778878899999874
No 17
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=41.15 E-value=9 Score=33.69 Aligned_cols=32 Identities=25% Similarity=0.488 Sum_probs=23.5
Q ss_pred CccccCCCCCCCCCCCCCCCCCcccchhhhhhh
Q 019919 226 VRKCLHCASEKTPQWRTGPMGPKTLCNACGVRY 258 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlry 258 (334)
-..|..|+...|-.=+.+- ---.-|+|||-..
T Consensus 97 yVlC~~C~sPdT~l~k~~r-~~~l~C~ACGa~~ 128 (133)
T TIGR00311 97 YVICRECNRPDTRIIKEGR-VSLLKCEACGAKA 128 (133)
T ss_pred eEECCCCCCCCcEEEEeCC-eEEEecccCCCCC
Confidence 4789999999998877532 1124899999643
No 18
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=38.42 E-value=12 Score=25.86 Aligned_cols=32 Identities=25% Similarity=0.655 Sum_probs=25.4
Q ss_pred ccccCCCCC-CCCCCCCCCCCCcccchhhhhhh
Q 019919 227 RKCLHCASE-KTPQWRTGPMGPKTLCNACGVRY 258 (334)
Q Consensus 227 ~~C~~C~~~-~TP~WR~GP~G~ktLCNACGlry 258 (334)
..|.+|++. .-+..+-.+.|.+..|-.||-.|
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 468889886 46888888888888999998655
No 19
>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=37.35 E-value=15 Score=36.17 Aligned_cols=35 Identities=26% Similarity=0.607 Sum_probs=25.2
Q ss_pred CCccccCCCCCCCCCC----CCCCCCCc--ccchhhhhhhh
Q 019919 225 SVRKCLHCASEKTPQW----RTGPMGPK--TLCNACGVRYK 259 (334)
Q Consensus 225 ~~~~C~~C~~~~TP~W----R~GP~G~k--tLCNACGlryk 259 (334)
+...|..|+-.+.-.| |...++-. ..|..||-+|+
T Consensus 257 ~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 4689999998776555 54444422 38999999986
No 20
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=36.87 E-value=11 Score=32.02 Aligned_cols=30 Identities=27% Similarity=0.417 Sum_probs=22.4
Q ss_pred CccccCCCCCCCCCCCCCCCCCcccchhhhh
Q 019919 226 VRKCLHCASEKTPQWRTGPMGPKTLCNACGV 256 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G~ktLCNACGl 256 (334)
-..|..|+...|-.=+.+- ---.-|+|||-
T Consensus 80 yVlC~~C~spdT~l~k~~r-~~~l~C~aCGa 109 (110)
T smart00653 80 YVLCPECGSPDTELIKENR-LFFLKCEACGA 109 (110)
T ss_pred cEECCCCCCCCcEEEEeCC-eEEEEccccCC
Confidence 4789999999998887621 11246999995
No 21
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=36.57 E-value=17 Score=27.69 Aligned_cols=23 Identities=30% Similarity=0.925 Sum_probs=18.6
Q ss_pred CCccccCCCCCCCCCCCCCCCCCcccchhhhh
Q 019919 225 SVRKCLHCASEKTPQWRTGPMGPKTLCNACGV 256 (334)
Q Consensus 225 ~~~~C~~C~~~~TP~WR~GP~G~ktLCNACGl 256 (334)
..-.|.+||..+-| ..+|..||.
T Consensus 26 ~l~~C~~CG~~~~~---------H~vC~~CG~ 48 (57)
T PRK12286 26 GLVECPNCGEPKLP---------HRVCPSCGY 48 (57)
T ss_pred cceECCCCCCccCC---------eEECCCCCc
Confidence 34579999988766 689999993
No 22
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=35.82 E-value=12 Score=34.64 Aligned_cols=33 Identities=21% Similarity=0.362 Sum_probs=24.5
Q ss_pred CccccCCCCCCCCCCCCCCCCCcccchhhhhhhh
Q 019919 226 VRKCLHCASEKTPQWRTGPMGPKTLCNACGVRYK 259 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk 259 (334)
-..|..|+...|-.=+.+- ---.-|+|||-..-
T Consensus 98 yV~C~~C~~pdT~l~k~~~-~~~l~C~aCGa~~~ 130 (201)
T PRK12336 98 YVICSECGLPDTRLVKEDR-VLMLRCDACGAHRP 130 (201)
T ss_pred eEECCCCCCCCcEEEEcCC-eEEEEcccCCCCcc
Confidence 4789999999998877631 11248999997654
No 23
>PHA02998 RNA polymerase subunit; Provisional
Probab=34.43 E-value=20 Score=33.66 Aligned_cols=34 Identities=26% Similarity=0.576 Sum_probs=27.7
Q ss_pred CccccCCCCCCCCCC----CCCCCCCc--ccchhhhhhhh
Q 019919 226 VRKCLHCASEKTPQW----RTGPMGPK--TLCNACGVRYK 259 (334)
Q Consensus 226 ~~~C~~C~~~~TP~W----R~GP~G~k--tLCNACGlryk 259 (334)
...|..|+-.++--| |.+.++.- ..|-.||-+|+
T Consensus 143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccC
Confidence 478999999887655 88877743 38999999998
No 24
>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=33.70 E-value=18 Score=27.10 Aligned_cols=30 Identities=20% Similarity=0.548 Sum_probs=21.9
Q ss_pred CccccCCCCCCCCCCCCCCCCCcccchhhhhhhh
Q 019919 226 VRKCLHCASEKTPQWRTGPMGPKTLCNACGVRYK 259 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk 259 (334)
...|..||....- ...+....|..||..+-
T Consensus 28 Sq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 28 SQTCPRCGHRNKK----RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred ccCccCccccccc----ccccceEEcCCCCCEEC
Confidence 4679999987654 44555689999998754
No 25
>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=32.77 E-value=15 Score=25.77 Aligned_cols=31 Identities=26% Similarity=0.711 Sum_probs=18.9
Q ss_pred cccCCCCCCCCCCCCCCCCCcccchhhhhhhhcC
Q 019919 228 KCLHCASEKTPQWRTGPMGPKTLCNACGVRYKSG 261 (334)
Q Consensus 228 ~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk~g 261 (334)
+|.+|+...+ .+- +.....+|..||+-+.-.
T Consensus 2 ~Cp~Cg~~~~-~~D--~~~g~~vC~~CG~Vl~e~ 32 (43)
T PF08271_consen 2 KCPNCGSKEI-VFD--PERGELVCPNCGLVLEEN 32 (43)
T ss_dssp SBTTTSSSEE-EEE--TTTTEEEETTT-BBEE-T
T ss_pred CCcCCcCCce-EEc--CCCCeEECCCCCCEeecc
Confidence 5899998762 222 222268999999876643
No 26
>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=29.86 E-value=28 Score=31.49 Aligned_cols=34 Identities=24% Similarity=0.462 Sum_probs=26.7
Q ss_pred cccCCCCCCCCCC--CCCCCCC----cccchhhhhhhhcC
Q 019919 228 KCLHCASEKTPQW--RTGPMGP----KTLCNACGVRYKSG 261 (334)
Q Consensus 228 ~C~~C~~~~TP~W--R~GP~G~----ktLCNACGlryk~g 261 (334)
+|..|+...|-.- |....|. +--|.+||-||-.-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTy 41 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTF 41 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcccee
Confidence 6999999998777 6666663 35899999999753
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=29.49 E-value=32 Score=28.75 Aligned_cols=33 Identities=30% Similarity=0.770 Sum_probs=27.6
Q ss_pred CccccCCCCCCCCCCCCCCCCCcccchhhhhhhhc
Q 019919 226 VRKCLHCASEKTPQWRTGPMGPKTLCNACGVRYKS 260 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk~ 260 (334)
.+.|..|+. .-|+|=.=..| -.||-.|.-.-+.
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 56999888888 7999999877664
No 28
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=29.05 E-value=28 Score=34.38 Aligned_cols=30 Identities=30% Similarity=0.607 Sum_probs=23.3
Q ss_pred CCccccCCCCCCCCCCCCCCCCCcccchhhhhhh
Q 019919 225 SVRKCLHCASEKTPQWRTGPMGPKTLCNACGVRY 258 (334)
Q Consensus 225 ~~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlry 258 (334)
..|-|.+||+...|. ..|-+.+|+.||.++
T Consensus 110 ~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~ 139 (279)
T COG2816 110 SHRFCGRCGTKTYPR----EGGWARVCPKCGHEH 139 (279)
T ss_pred hCcCCCCCCCcCccc----cCceeeeCCCCCCcc
Confidence 467899999887763 345678999999876
No 29
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=28.81 E-value=21 Score=25.13 Aligned_cols=32 Identities=22% Similarity=0.673 Sum_probs=22.1
Q ss_pred cccCCCCCCCCCC----CCCCCCCc--ccchhhhhhhh
Q 019919 228 KCLHCASEKTPQW----RTGPMGPK--TLCNACGVRYK 259 (334)
Q Consensus 228 ~C~~C~~~~TP~W----R~GP~G~k--tLCNACGlryk 259 (334)
.|..|+-.+.--| |.+.+|.. ..|-.||-+|+
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeC
Confidence 5888987664333 66666643 47999998876
No 30
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=28.79 E-value=32 Score=35.50 Aligned_cols=33 Identities=24% Similarity=0.723 Sum_probs=27.2
Q ss_pred CCccccCCCCCCCCCCCCCCCCCcccchhhhhhhh
Q 019919 225 SVRKCLHCASEKTPQWRTGPMGPKTLCNACGVRYK 259 (334)
Q Consensus 225 ~~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk 259 (334)
..++|..|+... |+|=.=..| -.||-.|.=.-+
T Consensus 21 gNk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHR 53 (395)
T PLN03114 21 DNKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHR 53 (395)
T ss_pred CCCcCccCCCCC-CCceeeccc-eeehhhhhHhhc
Confidence 468899999864 999888899 799999965544
No 31
>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=28.57 E-value=33 Score=31.47 Aligned_cols=35 Identities=20% Similarity=0.676 Sum_probs=25.7
Q ss_pred CCccccCCCCCCCCCCCC-------CCCCCcccchhhhhhhh
Q 019919 225 SVRKCLHCASEKTPQWRT-------GPMGPKTLCNACGVRYK 259 (334)
Q Consensus 225 ~~~~C~~C~~~~TP~WR~-------GP~G~ktLCNACGlryk 259 (334)
....|.+|.+..--.|-- ++.-....|+.||..|-
T Consensus 38 tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyP 79 (158)
T PF10083_consen 38 TITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYP 79 (158)
T ss_pred HHHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCc
Confidence 467899999887666632 44445679999999883
No 32
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=27.95 E-value=15 Score=24.71 Aligned_cols=33 Identities=24% Similarity=0.539 Sum_probs=22.0
Q ss_pred ccccCCCCCC-CCCCCCCCCCCcccchhhhhhhh
Q 019919 227 RKCLHCASEK-TPQWRTGPMGPKTLCNACGVRYK 259 (334)
Q Consensus 227 ~~C~~C~~~~-TP~WR~GP~G~ktLCNACGlryk 259 (334)
..|.+|++.- -+..+-+..|.+..|-.||..+.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 3688888853 34455555666788888887653
No 33
>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=27.18 E-value=19 Score=31.30 Aligned_cols=29 Identities=31% Similarity=0.588 Sum_probs=22.6
Q ss_pred ccccCCCCCCCCCCCCCCCCCcccchhhhh
Q 019919 227 RKCLHCASEKTPQWRTGPMGPKTLCNACGV 256 (334)
Q Consensus 227 ~~C~~C~~~~TP~WR~GP~G~ktLCNACGl 256 (334)
..|..|+...|-.=+.+..= -.-|+|||-
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 67999999999887763222 468999995
No 34
>PF14122 YokU: YokU-like protein
Probab=26.79 E-value=22 Score=29.72 Aligned_cols=35 Identities=31% Similarity=0.805 Sum_probs=23.6
Q ss_pred cccCCCCCC-----CCCCCCCCCCCc---------ccchhhhhhhhcCC
Q 019919 228 KCLHCASEK-----TPQWRTGPMGPK---------TLCNACGVRYKSGR 262 (334)
Q Consensus 228 ~C~~C~~~~-----TP~WR~GP~G~k---------tLCNACGlryk~gr 262 (334)
.|..|+..+ +.....=|.|.+ ..|+.||+-|....
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~d~ 49 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQDDE 49 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEehhH
Confidence 488888864 333344566643 58999999997533
No 35
>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=26.06 E-value=33 Score=28.72 Aligned_cols=34 Identities=26% Similarity=0.628 Sum_probs=23.5
Q ss_pred CCccccCCCCCCCCCCCCCCCCCcccchhhhhhhhc
Q 019919 225 SVRKCLHCASEKTPQWRTGPMGPKTLCNACGVRYKS 260 (334)
Q Consensus 225 ~~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk~ 260 (334)
..+.|..|+.. -|+|-.=..| -.||-.|.-..+.
T Consensus 12 ~N~~CaDCg~~-~p~w~s~~~G-iflC~~Cag~HR~ 45 (116)
T PF01412_consen 12 GNKVCADCGAP-NPTWASLNYG-IFLCLECAGIHRS 45 (116)
T ss_dssp TCTB-TTT-SB-S--EEETTTT-EEE-HHHHHHHHH
T ss_pred CcCcCCCCCCC-CCCEEEeecC-hhhhHHHHHHHHH
Confidence 46899999954 4699888888 7999999987775
No 36
>COG3952 Predicted membrane protein [Function unknown]
Probab=25.55 E-value=18 Score=31.44 Aligned_cols=19 Identities=32% Similarity=0.427 Sum_probs=14.3
Q ss_pred CCCCCCCCCcccchhhhhhhh
Q 019919 239 QWRTGPMGPKTLCNACGVRYK 259 (334)
Q Consensus 239 ~WR~GP~G~ktLCNACGlryk 259 (334)
.||.+|-+ .||++||+.-.
T Consensus 76 i~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HHhcchHH--HHHHhhhHHHH
Confidence 35667766 89999999754
No 37
>PF15396 FAM60A: Protein Family FAM60A
Probab=25.54 E-value=26 Score=33.50 Aligned_cols=20 Identities=30% Similarity=0.509 Sum_probs=16.5
Q ss_pred cccchhhhhhhhcCCCCCCC
Q 019919 248 KTLCNACGVRYKSGRLVPEY 267 (334)
Q Consensus 248 ktLCNACGlryk~grllp~~ 267 (334)
+.+||||=|..|+-+.||.-
T Consensus 49 GeICNACVLLVKRwKKLP~G 68 (213)
T PF15396_consen 49 GEICNACVLLVKRWKKLPPG 68 (213)
T ss_pred chhhHHHHHHHHHHhhCCCC
Confidence 37999999999987777764
No 38
>PRK00420 hypothetical protein; Validated
Probab=25.28 E-value=36 Score=29.38 Aligned_cols=29 Identities=24% Similarity=0.608 Sum_probs=22.4
Q ss_pred CccccCCCCCCCCCCCCCCCCCcccchhhhhhhh
Q 019919 226 VRKCLHCASEKTPQWRTGPMGPKTLCNACGVRYK 259 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk 259 (334)
...|..|+ +|..|- ..| +..|-+||..+.
T Consensus 23 ~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCC---Ccceec-CCC-ceECCCCCCeee
Confidence 46788888 677764 344 799999999776
No 39
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=24.85 E-value=37 Score=30.60 Aligned_cols=33 Identities=30% Similarity=0.685 Sum_probs=22.4
Q ss_pred cccCCCCCCCCCC--CCCCCCC----cccchhhhhhhhc
Q 019919 228 KCLHCASEKTPQW--RTGPMGP----KTLCNACGVRYKS 260 (334)
Q Consensus 228 ~C~~C~~~~TP~W--R~GP~G~----ktLCNACGlryk~ 260 (334)
+|.+|+...|-.- |--+.|. ..-|.+||.+|..
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~ 40 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT 40 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence 6999998776544 2222242 2589999999864
No 40
>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=24.74 E-value=40 Score=24.01 Aligned_cols=27 Identities=30% Similarity=0.543 Sum_probs=19.1
Q ss_pred ccccCCCCCCCCCCCCCCCCCcccchhhhh
Q 019919 227 RKCLHCASEKTPQWRTGPMGPKTLCNACGV 256 (334)
Q Consensus 227 ~~C~~C~~~~TP~WR~GP~G~ktLCNACGl 256 (334)
..|.+|+.+ ..-|.++ .+ ...|++|+-
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 5555444 22 678999974
No 41
>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=24.69 E-value=38 Score=35.82 Aligned_cols=34 Identities=26% Similarity=0.784 Sum_probs=27.4
Q ss_pred CccccCCCCCCCCCCCC-------CCCCCcccchhhhhhhh
Q 019919 226 VRKCLHCASEKTPQWRT-------GPMGPKTLCNACGVRYK 259 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~-------GP~G~ktLCNACGlryk 259 (334)
-.+|-||+......|.. .|......|-.||-.+.
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred EccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCC
Confidence 58899999999998842 25556789999999875
No 42
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=23.85 E-value=14 Score=29.23 Aligned_cols=33 Identities=18% Similarity=0.339 Sum_probs=26.2
Q ss_pred ccccCCCCCCCCCCCCCCCCCcccchhhhhhhh
Q 019919 227 RKCLHCASEKTPQWRTGPMGPKTLCNACGVRYK 259 (334)
Q Consensus 227 ~~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk 259 (334)
-.|..|.++.|=+|++...=+-.-|-+||-.-+
T Consensus 11 A~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~ 43 (66)
T COG3529 11 AVCPACQAQDTLAMWRENNVEIVECVKCGHHMR 43 (66)
T ss_pred CCCcccchhhHHHHHHhcCCceEehhhcchHhh
Confidence 469999999997766655555789999998764
No 43
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=23.76 E-value=52 Score=20.97 Aligned_cols=23 Identities=30% Similarity=0.889 Sum_probs=14.8
Q ss_pred ccccCCCCCCCCCCCCCCCCCcccchhhhhh
Q 019919 227 RKCLHCASEKTPQWRTGPMGPKTLCNACGVR 257 (334)
Q Consensus 227 ~~C~~C~~~~TP~WR~GP~G~ktLCNACGlr 257 (334)
+.|.+|+....+. ...|..||..
T Consensus 3 ~~Cp~Cg~~~~~~--------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPD--------AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcc--------cccChhhCCC
Confidence 5688888854333 3567777754
No 44
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=23.09 E-value=25 Score=29.73 Aligned_cols=31 Identities=26% Similarity=0.717 Sum_probs=21.1
Q ss_pred CccccCCCCCCCCCCCCCCCCCcccchhhhhhhhcC
Q 019919 226 VRKCLHCASEKTPQWRTGPMGPKTLCNACGVRYKSG 261 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk~g 261 (334)
-.-|.-|+-..= - -.|...+|++||++|...
T Consensus 35 ~daCeiC~~~GY--~---q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 35 FDACEICGPKGY--Y---QEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred EEeccccCCCce--E---EECCEEEEecCCCEEehh
Confidence 456999943321 1 245579999999999753
No 45
>PRK05978 hypothetical protein; Provisional
Probab=22.30 E-value=51 Score=29.70 Aligned_cols=34 Identities=26% Similarity=0.609 Sum_probs=24.3
Q ss_pred CCccccCCCCCCCCCCCCCCCCCcccchhhhhhhhcC
Q 019919 225 SVRKCLHCASEKTPQWRTGPMGPKTLCNACGVRYKSG 261 (334)
Q Consensus 225 ~~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk~g 261 (334)
-..+|-+|+.-+ .++ |-..-..-|.+||+.|...
T Consensus 32 l~grCP~CG~G~--LF~-g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 32 FRGRCPACGEGK--LFR-AFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred HcCcCCCCCCCc--ccc-cccccCCCccccCCccccC
Confidence 456799998754 333 4555567899999999854
No 46
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=21.43 E-value=49 Score=23.00 Aligned_cols=26 Identities=31% Similarity=0.715 Sum_probs=19.1
Q ss_pred CccccCCCCCCCCCCCCCCCCCcccchhhhh
Q 019919 226 VRKCLHCASEKTPQWRTGPMGPKTLCNACGV 256 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G~ktLCNACGl 256 (334)
..+|..|+.. |-...+| ...|..||-
T Consensus 8 ~~~C~~C~~~----~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 8 NEPCPVCGSR----WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CCcCCCCCCe----EeEccCC-EEEhhhCce
Confidence 4569999887 5455567 789999984
No 47
>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=21.31 E-value=28 Score=23.04 Aligned_cols=29 Identities=31% Similarity=0.646 Sum_probs=15.2
Q ss_pred CccccCCCCCCCCCCCCCCCCCcccchhhhhhh
Q 019919 226 VRKCLHCASEKTPQWRTGPMGPKTLCNACGVRY 258 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlry 258 (334)
.+-|..||....+. +.|....|.+||..+
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 35688888766543 235577888888753
No 48
>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=21.25 E-value=70 Score=22.61 Aligned_cols=30 Identities=17% Similarity=0.491 Sum_probs=19.2
Q ss_pred ccccCCCCCCCCCCCCCCCCCcccchhhhh
Q 019919 227 RKCLHCASEKTPQWRTGPMGPKTLCNACGV 256 (334)
Q Consensus 227 ~~C~~C~~~~TP~WR~GP~G~ktLCNACGl 256 (334)
..|-.|+....=.|..-.......|+.||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 468888887765564422222578888874
No 49
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=21.01 E-value=42 Score=32.00 Aligned_cols=30 Identities=33% Similarity=0.565 Sum_probs=20.5
Q ss_pred CCccccCCCCCCCCCCCCCCCCCcccchhhhhhh
Q 019919 225 SVRKCLHCASEKTPQWRTGPMGPKTLCNACGVRY 258 (334)
Q Consensus 225 ~~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlry 258 (334)
..+-|.+||...... ..|.+..|.+||..+
T Consensus 98 ~~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 98 SHRFCGYCGHPMHPS----KTEWAMLCPHCRERY 127 (256)
T ss_pred cCccccccCCCCeec----CCceeEECCCCCCEE
Confidence 357799998865432 345567899998654
No 50
>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=20.57 E-value=45 Score=24.02 Aligned_cols=25 Identities=40% Similarity=0.860 Sum_probs=18.9
Q ss_pred CccccCCCCCCCCCCCCCCCCCcccchhhh
Q 019919 226 VRKCLHCASEKTPQWRTGPMGPKTLCNACG 255 (334)
Q Consensus 226 ~~~C~~C~~~~TP~WR~GP~G~ktLCNACG 255 (334)
...|..| .+|..| ...| +.+|-+|+
T Consensus 17 ~~~Cp~C---~~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDC---GTPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred cCccCCC---CCeeEE-ecCC-CEECCCCC
Confidence 4578888 589998 2345 78999986
No 51
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.23 E-value=47 Score=29.48 Aligned_cols=33 Identities=24% Similarity=0.556 Sum_probs=22.7
Q ss_pred CCccccCCCCCCCCCCCCCCCCCcccchhhhhhhhc
Q 019919 225 SVRKCLHCASEKTPQWRTGPMGPKTLCNACGVRYKS 260 (334)
Q Consensus 225 ~~~~C~~C~~~~TP~WR~GP~G~ktLCNACGlryk~ 260 (334)
-.-+|-+|+--+- =+|=.-...-|.|||+.|-.
T Consensus 20 l~grCP~CGeGrL---F~gFLK~~p~C~aCG~dyg~ 52 (126)
T COG5349 20 LRGRCPRCGEGRL---FRGFLKVVPACEACGLDYGF 52 (126)
T ss_pred hcCCCCCCCCchh---hhhhcccCchhhhccccccC
Confidence 4568999996441 22334445789999999974
Done!