Query 017390
Match_columns 372
No_of_seqs 224 out of 796
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 08:09:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017390.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017390hhsearch_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 2E-14 4.3E-19 108.6 3.4 44 257-303 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.4 6.4E-14 1.4E-18 104.8 3.6 48 254-303 2-49 (52)
3 PF00320 GATA: GATA zinc finge 99.3 2.7E-13 5.8E-18 94.5 0.6 34 258-291 1-34 (36)
4 KOG1601 GATA-4/5/6 transcripti 99.1 4.6E-10 9.9E-15 99.6 11.6 49 255-303 199-250 (340)
5 COG5641 GAT1 GATA Zn-finger-co 98.4 1.7E-07 3.6E-12 97.7 2.3 52 256-310 159-215 (498)
6 KOG3554 Histone deacetylase co 90.5 0.17 3.7E-06 53.6 2.5 36 254-289 385-422 (693)
7 PRK12286 rpmF 50S ribosomal pr 86.1 0.56 1.2E-05 36.2 2.2 26 253-287 25-50 (57)
8 COG5641 GAT1 GATA Zn-finger-co 81.9 0.85 1.8E-05 48.6 2.1 35 255-289 297-332 (498)
9 PRK14892 putative transcriptio 79.2 1.3 2.8E-05 37.8 1.9 35 254-289 20-54 (99)
10 PF01783 Ribosomal_L32p: Ribos 78.2 0.42 9.1E-06 36.4 -1.1 25 254-288 25-49 (56)
11 TIGR01031 rpmF_bact ribosomal 72.5 2.6 5.7E-05 32.3 1.9 26 253-288 24-49 (55)
12 PRK01110 rpmF 50S ribosomal pr 64.8 3.5 7.6E-05 32.1 1.2 26 253-288 25-50 (60)
13 PRK03988 translation initiatio 56.4 3.8 8.2E-05 36.8 0.1 32 255-287 102-133 (138)
14 PF14803 Nudix_N_2: Nudix N-te 56.3 3.7 8E-05 28.8 -0.0 30 256-285 1-30 (34)
15 TIGR00311 aIF-2beta translatio 53.8 4.4 9.6E-05 36.1 0.1 32 255-287 97-128 (133)
16 smart00653 eIF2B_5 domain pres 51.7 5 0.00011 34.7 0.1 29 256-285 81-109 (110)
17 PRK12336 translation initiatio 48.0 6.1 0.00013 37.2 0.0 33 255-288 98-130 (201)
18 COG5347 GTPase-activating prot 45.1 10 0.00022 38.4 1.1 35 253-289 18-52 (319)
19 KOG3740 Uncharacterized conser 44.8 8.9 0.00019 42.3 0.7 36 254-289 461-499 (706)
20 COG4888 Uncharacterized Zn rib 44.5 12 0.00025 32.6 1.2 46 255-305 22-69 (104)
21 PF08271 TF_Zn_Ribbon: TFIIB z 44.1 8.2 0.00018 27.5 0.2 30 257-289 2-31 (43)
22 COG3529 Predicted nucleic-acid 41.5 5.9 0.00013 31.7 -0.9 35 254-288 9-43 (66)
23 smart00105 ArfGap Putative GTP 40.7 26 0.00056 29.7 2.7 50 254-305 2-52 (112)
24 PF01873 eIF-5_eIF-2B: Domain 39.8 9.5 0.00021 33.6 -0.0 29 256-285 94-122 (125)
25 COG0333 RpmF Ribosomal protein 38.3 13 0.00028 29.1 0.5 24 254-286 26-49 (57)
26 PF01412 ArfGap: Putative GTPa 37.9 22 0.00047 30.4 1.8 34 254-289 12-45 (116)
27 PF09538 FYDLN_acid: Protein o 37.0 19 0.00042 31.1 1.4 26 274-303 6-31 (108)
28 COG2816 NPY1 NTP pyrophosphohy 34.4 21 0.00046 35.7 1.4 31 254-288 110-140 (279)
29 PF01096 TFIIS_C: Transcriptio 33.4 9.1 0.0002 27.1 -1.0 32 257-288 2-39 (39)
30 TIGR00244 transcriptional regu 33.1 22 0.00048 32.6 1.2 34 256-289 1-40 (147)
31 PF09526 DUF2387: Probable met 31.5 16 0.00034 29.5 -0.0 36 254-289 7-42 (71)
32 PF06677 Auto_anti-p27: Sjogre 31.3 22 0.00047 26.0 0.7 26 254-284 16-41 (41)
33 PLN03114 ADP-ribosylation fact 30.9 41 0.00089 35.2 2.8 48 254-303 21-69 (395)
34 TIGR01385 TFSII transcription 30.4 20 0.00044 35.9 0.5 35 254-288 257-297 (299)
35 PF04810 zf-Sec23_Sec24: Sec23 29.0 27 0.0006 24.7 0.9 32 255-286 2-33 (40)
36 PF07282 OrfB_Zn_ribbon: Putat 28.8 24 0.00051 27.0 0.6 31 254-288 27-57 (69)
37 PF10083 DUF2321: Uncharacteri 26.8 33 0.00071 31.9 1.2 35 254-288 38-79 (158)
38 PRK00420 hypothetical protein; 26.3 30 0.00066 30.3 0.9 30 254-288 22-51 (112)
39 PF05129 Elf1: Transcription e 25.8 17 0.00037 29.8 -0.8 35 254-289 21-58 (81)
40 PF12760 Zn_Tnp_IS1595: Transp 25.3 34 0.00074 24.7 0.8 28 255-285 18-45 (46)
41 PHA02998 RNA polymerase subuni 23.7 33 0.00072 32.7 0.7 34 254-288 142-182 (195)
42 PF13717 zinc_ribbon_4: zinc-r 23.3 26 0.00057 24.5 -0.1 31 257-287 4-35 (36)
43 smart00440 ZnF_C2C2 C2C2 Zinc 23.1 29 0.00062 24.8 0.1 32 257-288 2-39 (40)
44 PF09297 zf-NADH-PPase: NADH p 22.9 20 0.00044 24.0 -0.7 29 255-287 3-31 (32)
45 PRK00464 nrdR transcriptional 22.8 41 0.00088 30.8 1.0 34 256-289 1-40 (154)
46 KOG1598 Transcription initiati 22.2 47 0.001 36.0 1.5 31 256-289 1-31 (521)
47 COG3952 Predicted membrane pro 21.1 23 0.00051 31.1 -0.8 18 269-288 77-94 (113)
48 TIGR02443 conserved hypothetic 20.5 34 0.00074 27.1 0.1 35 254-288 8-42 (59)
49 PF13248 zf-ribbon_3: zinc-rib 20.1 58 0.0013 21.0 1.1 23 256-286 3-25 (26)
50 KOG0909 Peptide:N-glycanase [P 20.0 51 0.0011 35.3 1.2 35 254-288 160-205 (500)
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=99.48 E-value=2e-14 Score=108.55 Aligned_cols=44 Identities=48% Similarity=0.962 Sum_probs=39.9
Q ss_pred ccccCCCCCCCccccCCCCCcccchhhhhhhhhCCCCCCCCCCCCCc
Q 017390 257 KCLHCATDKTPQWRTGPMGPKTLCNACGVRYKSGRLVPEYRPASSPT 303 (372)
Q Consensus 257 ~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk~~rl~p~~RP~~~pt 303 (372)
.|+||++++||+||+||.|..+||||||+||++. ...||+..+.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~---~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKH---GVMRPLSKRK 44 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhc---CCCCCcccCc
Confidence 5999999999999999988899999999999964 4789988876
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.44 E-value=6.4e-14 Score=104.79 Aligned_cols=48 Identities=52% Similarity=0.998 Sum_probs=39.6
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhhhhhhhhCCCCCCCCCCCCCc
Q 017390 254 EGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYKSGRLVPEYRPASSPT 303 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk~~rl~p~~RP~~~pt 303 (372)
..++|+||+++.||+||+||.|..+||||||++|++.+.+ +||+.+.+
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~--~rp~~~~~ 49 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL--KRPLSLKK 49 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC--CCcccccc
Confidence 3578999999999999999999889999999999975432 46665543
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=99.32 E-value=2.7e-13 Score=94.52 Aligned_cols=34 Identities=59% Similarity=1.239 Sum_probs=27.2
Q ss_pred cccCCCCCCCccccCCCCCcccchhhhhhhhhCC
Q 017390 258 CLHCATDKTPQWRTGPMGPKTLCNACGVRYKSGR 291 (372)
Q Consensus 258 C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk~~r 291 (372)
|.||++++||+||+||.|..+||||||++|++.+
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~ 34 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYG 34 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhC
Confidence 8999999999999999998889999999999754
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=99.14 E-value=4.6e-10 Score=99.63 Aligned_cols=49 Identities=67% Similarity=1.306 Sum_probs=43.7
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhhhhhhhhC---CCCCCCCCCCCCc
Q 017390 255 GRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYKSG---RLVPEYRPASSPT 303 (372)
Q Consensus 255 ~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk~~---rl~p~~RP~~~pt 303 (372)
...|.+|+++.||+||+++.|++.+|||||++|+++ +.++.++....++
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~ 250 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPR 250 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCccccccccCcccccc
Confidence 589999999999999999999999999999999997 6677777766655
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.35 E-value=1.7e-07 Score=97.70 Aligned_cols=52 Identities=37% Similarity=0.655 Sum_probs=48.0
Q ss_pred cccccCCCCCCCccccCCCC----CcccchhhhhhhhhCCCCCCCC-CCCCCcccccccc
Q 017390 256 RKCLHCATDKTPQWRTGPMG----PKTLCNACGVRYKSGRLVPEYR-PASSPTFVLTKHS 310 (372)
Q Consensus 256 r~C~~C~t~~TP~WR~GP~G----~~tLCNACGl~yk~~rl~p~~R-P~~~pt~~~~~~s 310 (372)
..|.+|.++.||+|||+..+ .-+|||||||+|+ +|...| |+++++.++..|.
T Consensus 159 ~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~k---lhg~~r~P~t~ks~~~ks~~ 215 (498)
T COG5641 159 HVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLK---LHGSPRAPISLKSDSIKSRS 215 (498)
T ss_pred chhccccccCCccccccccccccCCcccccccccccc---ccCCcCCCcccccccccccc
Confidence 48999999999999999993 2899999999999 899999 9999999999877
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=90.55 E-value=0.17 Score=53.56 Aligned_cols=36 Identities=33% Similarity=0.726 Sum_probs=31.5
Q ss_pred CCcccccCCCCCCCcc--ccCCCCCcccchhhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQW--RTGPMGPKTLCNACGVRYKS 289 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~W--R~GP~G~~tLCNACGl~yk~ 289 (372)
.++.|.+|++++.-+| .-+|.-.+.||-.|-+||||
T Consensus 385 ~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKK 422 (693)
T KOG3554|consen 385 DGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKK 422 (693)
T ss_pred CCCcccccccccccceeccCCCCccchhhHHHHHHHHH
Confidence 5789999999999999 55666667899999999998
No 7
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=86.10 E-value=0.56 Score=36.24 Aligned_cols=26 Identities=27% Similarity=0.648 Sum_probs=20.7
Q ss_pred CCCcccccCCCCCCCccccCCCCCcccchhhhhhh
Q 017390 253 GEGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRY 287 (372)
Q Consensus 253 ~~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~y 287 (372)
...-.|.+||...-| ..+|..||.|-
T Consensus 25 ~~l~~C~~CG~~~~~---------H~vC~~CG~Y~ 50 (57)
T PRK12286 25 PGLVECPNCGEPKLP---------HRVCPSCGYYK 50 (57)
T ss_pred CcceECCCCCCccCC---------eEECCCCCcCC
Confidence 466789999987765 78999999543
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=81.95 E-value=0.85 Score=48.59 Aligned_cols=35 Identities=31% Similarity=0.454 Sum_probs=29.2
Q ss_pred CcccccCCC-CCCCccccCCCCCcccchhhhhhhhh
Q 017390 255 GRKCLHCAT-DKTPQWRTGPMGPKTLCNACGVRYKS 289 (372)
Q Consensus 255 ~r~C~~C~t-~~TP~WR~GP~G~~tLCNACGl~yk~ 289 (372)
...|.+|.+ +.||.||+...-.-++|||||++.+.
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~ 332 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKP 332 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCC
Confidence 557888887 67899988887778999999999984
No 9
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=79.16 E-value=1.3 Score=37.84 Aligned_cols=35 Identities=14% Similarity=0.195 Sum_probs=23.5
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYKS 289 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk~ 289 (372)
..-.|.+|+...-+.=+ +-..+...|-.||.|+.+
T Consensus 20 t~f~CP~Cge~~v~v~~-~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGKVSISVKI-KKNIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCCeEeeeec-CCCcceEECCCCCCccCE
Confidence 45689999954322211 223458999999999875
No 10
>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=78.21 E-value=0.42 Score=36.42 Aligned_cols=25 Identities=40% Similarity=0.933 Sum_probs=19.1
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYK 288 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk 288 (372)
....|.+||...- ++.+|.+|| +|+
T Consensus 25 ~l~~c~~cg~~~~---------~H~vc~~cG-~y~ 49 (56)
T PF01783_consen 25 NLVKCPNCGEPKL---------PHRVCPSCG-YYK 49 (56)
T ss_dssp SEEESSSSSSEES---------TTSBCTTTB-BSS
T ss_pred ceeeeccCCCEec---------ccEeeCCCC-eEC
Confidence 6678999996432 378999999 555
No 11
>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=72.51 E-value=2.6 Score=32.28 Aligned_cols=26 Identities=35% Similarity=0.752 Sum_probs=19.5
Q ss_pred CCCcccccCCCCCCCccccCCCCCcccchhhhhhhh
Q 017390 253 GEGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYK 288 (372)
Q Consensus 253 ~~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk 288 (372)
...-.|.+||...- +..+|-.|| +|+
T Consensus 24 p~l~~C~~cG~~~~---------~H~vc~~cG-~Y~ 49 (55)
T TIGR01031 24 PTLVVCPNCGEFKL---------PHRVCPSCG-YYK 49 (55)
T ss_pred CcceECCCCCCccc---------CeeECCccC-eEC
Confidence 46678999998543 378999999 444
No 12
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=64.78 E-value=3.5 Score=32.15 Aligned_cols=26 Identities=8% Similarity=-0.133 Sum_probs=18.9
Q ss_pred CCCcccccCCCCCCCccccCCCCCcccchhhhhhhh
Q 017390 253 GEGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYK 288 (372)
Q Consensus 253 ~~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk 288 (372)
.....|.+|+...-| +.+|. ||.|.-
T Consensus 25 ~~~~~c~~cg~~~~p---------H~vc~-cG~Y~g 50 (60)
T PRK01110 25 PTLSVDKTTGEYHLP---------HHVSP-KGYYKG 50 (60)
T ss_pred CceeEcCCCCceecc---------ceecC-CcccCC
Confidence 356789999987654 67899 995543
No 13
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=56.41 E-value=3.8 Score=36.79 Aligned_cols=32 Identities=25% Similarity=0.485 Sum_probs=24.4
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhhhhhh
Q 017390 255 GRKCLHCATDKTPQWRTGPMGPKTLCNACGVRY 287 (372)
Q Consensus 255 ~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~y 287 (372)
=-.|..|+.+.|-+=+.+-.= -..|+|||-..
T Consensus 102 yVlC~~C~spdT~l~k~~r~~-~l~C~ACGa~~ 133 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGRIW-VLKCEACGAET 133 (138)
T ss_pred cEECCCCCCCCcEEEEcCCeE-EEEcccCCCCC
Confidence 468999999999998753322 46899999653
No 14
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=56.29 E-value=3.7 Score=28.81 Aligned_cols=30 Identities=23% Similarity=0.572 Sum_probs=15.6
Q ss_pred cccccCCCCCCCccccCCCCCcccchhhhh
Q 017390 256 RKCLHCATDKTPQWRTGPMGPKTLCNACGV 285 (372)
Q Consensus 256 r~C~~C~t~~TP~WR~GP~G~~tLCNACGl 285 (372)
+-|.+||..-+-.--.|..-.+.+|.+||.
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 358999987543334566666789999984
No 15
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=53.82 E-value=4.4 Score=36.15 Aligned_cols=32 Identities=25% Similarity=0.507 Sum_probs=23.9
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhhhhhh
Q 017390 255 GRKCLHCATDKTPQWRTGPMGPKTLCNACGVRY 287 (372)
Q Consensus 255 ~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~y 287 (372)
=-.|..|+.+.|-+-+.+-.- -..|+|||-..
T Consensus 97 yVlC~~C~sPdT~l~k~~r~~-~l~C~ACGa~~ 128 (133)
T TIGR00311 97 YVICRECNRPDTRIIKEGRVS-LLKCEACGAKA 128 (133)
T ss_pred eEECCCCCCCCcEEEEeCCeE-EEecccCCCCC
Confidence 357999999999988754321 35899999653
No 16
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=51.67 E-value=5 Score=34.67 Aligned_cols=29 Identities=24% Similarity=0.500 Sum_probs=22.7
Q ss_pred cccccCCCCCCCccccCCCCCcccchhhhh
Q 017390 256 RKCLHCATDKTPQWRTGPMGPKTLCNACGV 285 (372)
Q Consensus 256 r~C~~C~t~~TP~WR~GP~G~~tLCNACGl 285 (372)
-.|..|+.+.|-+=+.+-.= -.-|+|||-
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 67999999999998873222 346999995
No 17
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=47.97 E-value=6.1 Score=37.18 Aligned_cols=33 Identities=21% Similarity=0.367 Sum_probs=25.1
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhhhhhhh
Q 017390 255 GRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYK 288 (372)
Q Consensus 255 ~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk 288 (372)
=-.|..|+.+.|-+-+.+..= -.-|+|||-..-
T Consensus 98 yV~C~~C~~pdT~l~k~~~~~-~l~C~aCGa~~~ 130 (201)
T PRK12336 98 YVICSECGLPDTRLVKEDRVL-MLRCDACGAHRP 130 (201)
T ss_pred eEECCCCCCCCcEEEEcCCeE-EEEcccCCCCcc
Confidence 367999999999998764221 358999997654
No 18
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=45.05 E-value=10 Score=38.41 Aligned_cols=35 Identities=29% Similarity=0.725 Sum_probs=30.4
Q ss_pred CCCcccccCCCCCCCccccCCCCCcccchhhhhhhhh
Q 017390 253 GEGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYKS 289 (372)
Q Consensus 253 ~~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk~ 289 (372)
...+.|+.|+... |+|-.=..| -.||--|----+.
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 3668999999999 999999999 8999999766553
No 19
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=44.83 E-value=8.9 Score=42.28 Aligned_cols=36 Identities=28% Similarity=0.655 Sum_probs=29.6
Q ss_pred CCcccccCCCCCCCccccCCCC---Ccccchhhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQWRTGPMG---PKTLCNACGVRYKS 289 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G---~~tLCNACGl~yk~ 289 (372)
+.-.|..|.+.-||.|+.-+.+ .+.+|.+|-.--.+
T Consensus 461 ~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSnqk 499 (706)
T KOG3740|consen 461 EPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSNQK 499 (706)
T ss_pred CchhhhhcccccccccccccccCcchHHHHHhhhhhccc
Confidence 5678999999999999887766 46899999765554
No 20
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=44.49 E-value=12 Score=32.59 Aligned_cols=46 Identities=22% Similarity=0.449 Sum_probs=29.8
Q ss_pred CcccccCCCCCCCc--cccCCCCCcccchhhhhhhhhCCCCCCCCCCCCCccc
Q 017390 255 GRKCLHCATDKTPQ--WRTGPMGPKTLCNACGVRYKSGRLVPEYRPASSPTFV 305 (372)
Q Consensus 255 ~r~C~~C~t~~TP~--WR~GP~G~~tLCNACGl~yk~~rl~p~~RP~~~pt~~ 305 (372)
.-.|.+|+..+-.+ -.++-...-..|-.||++|.- +.+++.+|-++
T Consensus 22 ~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~-----ev~~l~~~vDv 69 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFEC-----EVPELSEPVDV 69 (104)
T ss_pred eEecCccCCeeeeEEEEEecCceeEEEcccCcceEEE-----eccccccchhH
Confidence 35799999876442 344444436799999999984 34455555443
No 21
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=44.11 E-value=8.2 Score=27.50 Aligned_cols=30 Identities=23% Similarity=0.694 Sum_probs=19.7
Q ss_pred ccccCCCCCCCccccCCCCCcccchhhhhhhhh
Q 017390 257 KCLHCATDKTPQWRTGPMGPKTLCNACGVRYKS 289 (372)
Q Consensus 257 ~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk~ 289 (372)
+|.+|+... -.+ .--.| ..+|..||+-..-
T Consensus 2 ~Cp~Cg~~~-~~~-D~~~g-~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKE-IVF-DPERG-ELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSE-EEE-ETTTT-EEEETTT-BBEE-
T ss_pred CCcCCcCCc-eEE-cCCCC-eEECCCCCCEeec
Confidence 699999976 222 23344 7899999987764
No 22
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=41.48 E-value=5.9 Score=31.66 Aligned_cols=35 Identities=20% Similarity=0.370 Sum_probs=26.9
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYK 288 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk 288 (372)
.+..|-.|.+..|-+|.+-..-...-|.+||..-+
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 45689999999997654444444889999998775
No 23
>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=40.70 E-value=26 Score=29.74 Aligned_cols=50 Identities=24% Similarity=0.541 Sum_probs=36.6
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhhhhhhhhCCCC-CCCCCCCCCccc
Q 017390 254 EGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYKSGRLV-PEYRPASSPTFV 305 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk~~rl~-p~~RP~~~pt~~ 305 (372)
..+.|+.|+. .-|+|-.=..| -.||-.|.-.-+.-..| ...|.++|-++.
T Consensus 2 ~N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~lg~his~VkSl~md~w~ 52 (112)
T smart00105 2 GNKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRSLGVHISKVRSLTLDTWT 52 (112)
T ss_pred CCCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHhcCCCcCeeeecccCCCC
Confidence 3578999998 55999988889 89999998887752222 235667665443
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=39.83 E-value=9.5 Score=33.64 Aligned_cols=29 Identities=28% Similarity=0.578 Sum_probs=23.7
Q ss_pred cccccCCCCCCCccccCCCCCcccchhhhh
Q 017390 256 RKCLHCATDKTPQWRTGPMGPKTLCNACGV 285 (372)
Q Consensus 256 r~C~~C~t~~TP~WR~GP~G~~tLCNACGl 285 (372)
-.|..|+...|-+-+.+..- -.-|+|||-
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 57999999999998875443 578999995
No 25
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=38.31 E-value=13 Score=29.12 Aligned_cols=24 Identities=29% Similarity=0.668 Sum_probs=18.2
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhhhhh
Q 017390 254 EGRKCLHCATDKTPQWRTGPMGPKTLCNACGVR 286 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~ 286 (372)
..-.|.+||...-| ..+|-.||.|
T Consensus 26 ~~~~c~~cG~~~l~---------Hrvc~~cg~Y 49 (57)
T COG0333 26 TLSVCPNCGEYKLP---------HRVCLKCGYY 49 (57)
T ss_pred cceeccCCCCcccC---------ceEcCCCCCc
Confidence 35789999987643 6799999954
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=37.86 E-value=22 Score=30.35 Aligned_cols=34 Identities=26% Similarity=0.638 Sum_probs=24.5
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYKS 289 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk~ 289 (372)
+.+.|+.|+... |.|-.=..| -.||-.|.-..+.
T Consensus 12 ~N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~ 45 (116)
T PF01412_consen 12 GNKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRS 45 (116)
T ss_dssp TCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHH
T ss_pred CcCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHH
Confidence 568999999554 699998899 8999999988875
No 27
>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=37.00 E-value=19 Score=31.08 Aligned_cols=26 Identities=27% Similarity=0.746 Sum_probs=14.5
Q ss_pred CCCcccchhhhhhhhhCCCCCCCCCCCCCc
Q 017390 274 MGPKTLCNACGVRYKSGRLVPEYRPASSPT 303 (372)
Q Consensus 274 ~G~~tLCNACGl~yk~~rl~p~~RP~~~pt 303 (372)
.|-|.+|..||.+|- -|.. .|+..|+
T Consensus 6 lGtKR~Cp~CG~kFY---DLnk-~PivCP~ 31 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFY---DLNK-DPIVCPK 31 (108)
T ss_pred cCCcccCCCCcchhc---cCCC-CCccCCC
Confidence 355667777777666 3333 4444443
No 28
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=34.36 E-value=21 Score=35.73 Aligned_cols=31 Identities=29% Similarity=0.540 Sum_probs=24.3
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYK 288 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk 288 (372)
..|-|.+||+...+. ..|-+.+|+.||.++.
T Consensus 110 ~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~f 140 (279)
T COG2816 110 SHRFCGRCGTKTYPR----EGGWARVCPKCGHEHF 140 (279)
T ss_pred hCcCCCCCCCcCccc----cCceeeeCCCCCCccC
Confidence 457899999988763 3455789999998876
No 29
>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=33.37 E-value=9.1 Score=27.14 Aligned_cols=32 Identities=25% Similarity=0.676 Sum_probs=20.1
Q ss_pred ccccCCCCCCCcc----ccCCCCCc--ccchhhhhhhh
Q 017390 257 KCLHCATDKTPQW----RTGPMGPK--TLCNACGVRYK 288 (372)
Q Consensus 257 ~C~~C~t~~TP~W----R~GP~G~~--tLCNACGl~yk 288 (372)
.|..|+...+--| |.+.++.- ..|..||-+|+
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 5888988774433 66666632 48999998874
No 30
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=33.14 E-value=22 Score=32.61 Aligned_cols=34 Identities=24% Similarity=0.495 Sum_probs=26.4
Q ss_pred cccccCCCCCCCcc--ccCCCCC----cccchhhhhhhhh
Q 017390 256 RKCLHCATDKTPQW--RTGPMGP----KTLCNACGVRYKS 289 (372)
Q Consensus 256 r~C~~C~t~~TP~W--R~GP~G~----~tLCNACGl~yk~ 289 (372)
++|-.|+...|-.- |....|. .-.|.+||.+|-.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTT 40 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTT 40 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccce
Confidence 47999999998876 5555652 3589999999864
No 31
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=31.51 E-value=16 Score=29.52 Aligned_cols=36 Identities=19% Similarity=0.298 Sum_probs=28.5
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYKS 289 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk~ 289 (372)
.+..|-.|....|-+|.+...-...-|-+||..-..
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 457899999999987655545657899999988773
No 32
>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=31.34 E-value=22 Score=25.96 Aligned_cols=26 Identities=38% Similarity=0.829 Sum_probs=19.8
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhhh
Q 017390 254 EGRKCLHCATDKTPQWRTGPMGPKTLCNACG 284 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G~~tLCNACG 284 (372)
....|..| .+|+.| ...| +.+|-+|+
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 34578888 589999 3456 78999996
No 33
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=30.94 E-value=41 Score=35.19 Aligned_cols=48 Identities=21% Similarity=0.540 Sum_probs=35.5
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhhhhhhhhCCC-CCCCCCCCCCc
Q 017390 254 EGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYKSGRL-VPEYRPASSPT 303 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk~~rl-~p~~RP~~~pt 303 (372)
..++|..|+... |.|-.=..| -.||-.|.-.-+.-+. +...|.++|-+
T Consensus 21 gNk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRsLGvHISfVRSltLD~ 69 (395)
T PLN03114 21 DNKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRSLGVHISFVRSTNLDS 69 (395)
T ss_pred CCCcCccCCCCC-CCceeeccc-eeehhhhhHhhccCCCCCceeecccCCC
Confidence 568999999865 999999999 8999999776664222 23456666644
No 34
>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=30.44 E-value=20 Score=35.94 Aligned_cols=35 Identities=26% Similarity=0.528 Sum_probs=25.2
Q ss_pred CCcccccCCCCCCCcc----ccCCCCC--cccchhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQW----RTGPMGP--KTLCNACGVRYK 288 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~W----R~GP~G~--~tLCNACGl~yk 288 (372)
....|..|+-...--| |...++- -+.|..||.+|+
T Consensus 257 ~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 5679999998876555 4444441 248999999997
No 35
>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=29.00 E-value=27 Score=24.74 Aligned_cols=32 Identities=25% Similarity=0.568 Sum_probs=21.0
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhhhhh
Q 017390 255 GRKCLHCATDKTPQWRTGPMGPKTLCNACGVR 286 (372)
Q Consensus 255 ~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~ 286 (372)
..+|.+|++---|.-+-...|..-.||-|+..
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 35899999999988887778877899999874
No 36
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=28.81 E-value=24 Score=26.95 Aligned_cols=31 Identities=19% Similarity=0.536 Sum_probs=23.3
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYK 288 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk 288 (372)
....|..||....- ...+....|..||..+-
T Consensus 27 TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK----RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCccCccccccc----ccccceEEcCCCCCEEC
Confidence 55789999987655 44455689999998765
No 37
>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=26.80 E-value=33 Score=31.91 Aligned_cols=35 Identities=23% Similarity=0.597 Sum_probs=25.8
Q ss_pred CCcccccCCCCCCCcccc-------CCCCCcccchhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQWRT-------GPMGPKTLCNACGVRYK 288 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~-------GP~G~~tLCNACGl~yk 288 (372)
....|.+|++..--.|-- ++.-....|+.||..|-
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 457899999987666632 44445679999999884
No 38
>PRK00420 hypothetical protein; Validated
Probab=26.34 E-value=30 Score=30.27 Aligned_cols=30 Identities=23% Similarity=0.573 Sum_probs=23.0
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYK 288 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk 288 (372)
....|..|+ +|+.|- ..| +..|-+||..+.
T Consensus 22 l~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCC---Ccceec-CCC-ceECCCCCCeee
Confidence 346788888 677774 345 899999999776
No 39
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=25.76 E-value=17 Score=29.81 Aligned_cols=35 Identities=20% Similarity=0.557 Sum_probs=17.4
Q ss_pred CCcccccCCCCCCCcc---ccCCCCCcccchhhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQW---RTGPMGPKTLCNACGVRYKS 289 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~W---R~GP~G~~tLCNACGl~yk~ 289 (372)
..-.|..|+..++=.- +.-.-| ..-|..||+.|..
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~-~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIG-ILSCRVCGESFQT 58 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEE-EEEESSS--EEEE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEE-EEEecCCCCeEEE
Confidence 3468999997665443 333334 6789999999985
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=25.27 E-value=34 Score=24.72 Aligned_cols=28 Identities=29% Similarity=0.595 Sum_probs=19.9
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhhhh
Q 017390 255 GRKCLHCATDKTPQWRTGPMGPKTLCNACGV 285 (372)
Q Consensus 255 ~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl 285 (372)
+..|.+|+.+ ..-|.++ .+ ...|++|+.
T Consensus 18 g~~CP~Cg~~-~~~~~~~-~~-~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGST-KHYRLKT-RG-RYRCKACRK 45 (46)
T ss_pred CCCCCCCCCe-eeEEeCC-CC-eEECCCCCC
Confidence 3679999998 4445444 33 789999974
No 41
>PHA02998 RNA polymerase subunit; Provisional
Probab=23.71 E-value=33 Score=32.70 Aligned_cols=34 Identities=21% Similarity=0.492 Sum_probs=27.6
Q ss_pred CCcccccCCCCCCCcc----ccCCCCCcc---cchhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQW----RTGPMGPKT---LCNACGVRYK 288 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~W----R~GP~G~~t---LCNACGl~yk 288 (372)
....|..|+-..+--| |.+.++ .| .|-.||.+|+
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEP-mT~FYkC~~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEP-PLVRHACRDCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCC-ceEEEEcCCCCCccC
Confidence 3468999999887655 877777 44 8999999998
No 42
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=23.29 E-value=26 Score=24.49 Aligned_cols=31 Identities=26% Similarity=0.653 Sum_probs=21.4
Q ss_pred ccccCCCCC-CCccccCCCCCcccchhhhhhh
Q 017390 257 KCLHCATDK-TPQWRTGPMGPKTLCNACGVRY 287 (372)
Q Consensus 257 ~C~~C~t~~-TP~WR~GP~G~~tLCNACGl~y 287 (372)
.|-+|++.- -+..+-.+.|....|-.||-.|
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 577777764 4666666777777788877654
No 43
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=23.10 E-value=29 Score=24.79 Aligned_cols=32 Identities=22% Similarity=0.626 Sum_probs=21.7
Q ss_pred ccccCCCCCCCcc----ccCCCCC--cccchhhhhhhh
Q 017390 257 KCLHCATDKTPQW----RTGPMGP--KTLCNACGVRYK 288 (372)
Q Consensus 257 ~C~~C~t~~TP~W----R~GP~G~--~tLCNACGl~yk 288 (372)
.|.+|+-...--| |...++. -..|-.||-+|+
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 5888987664433 6665552 248999998876
No 44
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=22.94 E-value=20 Score=24.05 Aligned_cols=29 Identities=28% Similarity=0.501 Sum_probs=15.9
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhhhhhh
Q 017390 255 GRKCLHCATDKTPQWRTGPMGPKTLCNACGVRY 287 (372)
Q Consensus 255 ~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~y 287 (372)
.+-|..||....+.. .|....|.+||..+
T Consensus 3 ~rfC~~CG~~t~~~~----~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAP----GGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--BEEE-S----SSS-EEESSSS-EE
T ss_pred CcccCcCCccccCCC----CcCEeECCCCcCEe
Confidence 367889988765442 35577899998753
No 45
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=22.83 E-value=41 Score=30.81 Aligned_cols=34 Identities=29% Similarity=0.645 Sum_probs=22.9
Q ss_pred cccccCCCCCCCcc--ccCCCC----Ccccchhhhhhhhh
Q 017390 256 RKCLHCATDKTPQW--RTGPMG----PKTLCNACGVRYKS 289 (372)
Q Consensus 256 r~C~~C~t~~TP~W--R~GP~G----~~tLCNACGl~yk~ 289 (372)
+.|-+|+...|-.- |--+.| ...-|.+||.+|..
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~ 40 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT 40 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence 46999999887653 211123 13689999999864
No 46
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=22.17 E-value=47 Score=36.01 Aligned_cols=31 Identities=26% Similarity=0.628 Sum_probs=21.9
Q ss_pred cccccCCCCCCCccccCCCCCcccchhhhhhhhh
Q 017390 256 RKCLHCATDKTPQWRTGPMGPKTLCNACGVRYKS 289 (372)
Q Consensus 256 r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk~ 289 (372)
+.|.||+.+.= . |+--.| ...|.+||.-..-
T Consensus 1 ~~C~~C~~s~f-e-~d~a~g-~~~C~~CG~v~E~ 31 (521)
T KOG1598|consen 1 MVCKNCGGSNF-E-RDEATG-NLYCTACGTVLEY 31 (521)
T ss_pred CcCCCCCCCCc-c-cccccC-Cceeccccceeec
Confidence 47999998652 1 222445 8999999998764
No 47
>COG3952 Predicted membrane protein [Function unknown]
Probab=21.05 E-value=23 Score=31.11 Aligned_cols=18 Identities=33% Similarity=0.486 Sum_probs=13.7
Q ss_pred cccCCCCCcccchhhhhhhh
Q 017390 269 WRTGPMGPKTLCNACGVRYK 288 (372)
Q Consensus 269 WR~GP~G~~tLCNACGl~yk 288 (372)
||.+|-+ .||++||++-.
T Consensus 77 ~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 77 RRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HhcchHH--HHHHhhhHHHH
Confidence 5666655 89999999765
No 48
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=20.54 E-value=34 Score=27.06 Aligned_cols=35 Identities=20% Similarity=0.359 Sum_probs=26.3
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhhhhhhh
Q 017390 254 EGRKCLHCATDKTPQWRTGPMGPKTLCNACGVRYK 288 (372)
Q Consensus 254 ~~r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~yk 288 (372)
.+..|-.|....|-+|.+...-...-|-.||..-.
T Consensus 8 AGA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~ 42 (59)
T TIGR02443 8 AGAVCPACSAQDTLAMWKENNIELVECVECGYQEQ 42 (59)
T ss_pred ccccCCCCcCccEEEEEEeCCceEEEeccCCCccc
Confidence 45789999999987654433334789999998776
No 49
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=20.13 E-value=58 Score=21.04 Aligned_cols=23 Identities=26% Similarity=0.869 Sum_probs=14.0
Q ss_pred cccccCCCCCCCccccCCCCCcccchhhhhh
Q 017390 256 RKCLHCATDKTPQWRTGPMGPKTLCNACGVR 286 (372)
Q Consensus 256 r~C~~C~t~~TP~WR~GP~G~~tLCNACGl~ 286 (372)
+.|.+|+....+. ...|-.||..
T Consensus 3 ~~Cp~Cg~~~~~~--------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPD--------AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcc--------cccChhhCCC
Confidence 4688888754322 4567777753
No 50
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=20.01 E-value=51 Score=35.34 Aligned_cols=35 Identities=20% Similarity=0.486 Sum_probs=24.3
Q ss_pred CCcccccCCCCC-CCccccCCCCCc----------ccchhhhhhhh
Q 017390 254 EGRKCLHCATDK-TPQWRTGPMGPK----------TLCNACGVRYK 288 (372)
Q Consensus 254 ~~r~C~~C~t~~-TP~WR~GP~G~~----------tLCNACGl~yk 288 (372)
....|.+||... +++=+.+|.+.. +.||+||.--+
T Consensus 160 N~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~R 205 (500)
T KOG0909|consen 160 NNPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETR 205 (500)
T ss_pred CCCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCccc
Confidence 457899999887 444444454322 68999997655
Done!