Query 024757
Match_columns 263
No_of_seqs 205 out of 801
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 07:10:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024757.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024757hhsearch_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 5.1E-15 1.1E-19 106.9 3.2 44 166-212 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.5 1.4E-14 3.1E-19 103.6 3.6 47 163-211 2-48 (52)
3 PF00320 GATA: GATA zinc finge 99.4 6.3E-14 1.4E-18 93.5 -0.0 34 167-200 1-34 (36)
4 KOG1601 GATA-4/5/6 transcripti 99.0 3.2E-10 6.8E-15 95.0 4.1 49 164-212 199-250 (340)
5 COG5641 GAT1 GATA Zn-finger-co 98.4 1.6E-07 3.5E-12 93.4 2.5 54 163-219 157-215 (498)
6 KOG3554 Histone deacetylase co 89.9 0.17 3.7E-06 51.5 1.8 39 163-201 385-426 (693)
7 COG5641 GAT1 GATA Zn-finger-co 86.9 0.42 9.1E-06 48.5 2.4 43 164-209 297-340 (498)
8 PRK14892 putative transcriptio 73.0 2.4 5.3E-05 34.5 1.9 34 164-198 21-54 (99)
9 PF14803 Nudix_N_2: Nudix N-te 72.8 1.1 2.4E-05 29.9 -0.1 30 165-194 1-30 (34)
10 PRK03988 translation initiatio 65.2 2.2 4.8E-05 36.4 0.2 32 164-196 102-133 (138)
11 TIGR00311 aIF-2beta translatio 63.1 2.6 5.6E-05 35.8 0.2 32 164-196 97-128 (133)
12 PRK12286 rpmF 50S ribosomal pr 62.6 5.3 0.00012 29.4 1.7 24 164-196 27-50 (57)
13 PF01783 Ribosomal_L32p: Ribos 61.5 4.3 9.3E-05 29.4 1.1 25 163-197 25-49 (56)
14 smart00653 eIF2B_5 domain pres 60.7 3 6.5E-05 34.3 0.2 29 165-194 81-109 (110)
15 PRK12336 translation initiatio 57.6 3.6 7.8E-05 36.8 0.1 33 164-197 98-130 (201)
16 smart00105 ArfGap Putative GTP 56.1 9.8 0.00021 30.7 2.4 49 164-214 3-52 (112)
17 PF08271 TF_Zn_Ribbon: TFIIB z 50.3 6 0.00013 26.8 0.3 30 166-198 2-31 (43)
18 PF01873 eIF-5_eIF-2B: Domain 47.8 5.8 0.00013 33.3 -0.1 29 165-194 94-122 (125)
19 KOG0909 Peptide:N-glycanase [P 44.0 12 0.00025 38.2 1.3 33 165-197 162-205 (500)
20 PF09538 FYDLN_acid: Protein o 43.8 15 0.00032 30.3 1.6 14 184-197 7-20 (108)
21 KOG3740 Uncharacterized conser 43.7 9.8 0.00021 40.2 0.8 37 162-198 460-499 (706)
22 COG5347 GTPase-activating prot 43.0 12 0.00025 36.2 1.1 35 162-198 18-52 (319)
23 PRK01110 rpmF 50S ribosomal pr 43.0 16 0.00035 27.1 1.6 24 164-197 27-50 (60)
24 PF01412 ArfGap: Putative GTPa 41.8 14 0.00029 30.0 1.2 48 163-212 12-60 (116)
25 PLN03114 ADP-ribosylation fact 41.2 22 0.00048 35.5 2.7 49 163-213 21-70 (395)
26 PF07282 OrfB_Zn_ribbon: Putat 39.7 13 0.00028 26.9 0.7 31 163-197 27-57 (69)
27 PF13248 zf-ribbon_3: zinc-rib 39.5 18 0.00039 22.3 1.2 23 165-195 3-25 (26)
28 PF12760 Zn_Tnp_IS1595: Transp 37.9 18 0.00039 24.9 1.1 28 164-194 18-45 (46)
29 TIGR01031 rpmF_bact ribosomal 37.4 23 0.00049 25.8 1.6 23 164-195 26-48 (55)
30 COG2816 NPY1 NTP pyrophosphohy 37.3 17 0.00036 34.7 1.2 30 164-197 111-140 (279)
31 PF09297 zf-NADH-PPase: NADH p 37.2 7.6 0.00016 24.9 -0.8 29 164-196 3-31 (32)
32 PF01096 TFIIS_C: Transcriptio 36.9 7.7 0.00017 26.2 -0.8 32 166-197 2-39 (39)
33 PF05361 PP1_inhibitor: PKC-ac 35.1 17 0.00036 31.8 0.7 25 3-29 62-86 (144)
34 PF06677 Auto_anti-p27: Sjogre 31.3 24 0.00051 24.5 0.8 25 164-193 17-41 (41)
35 COG3529 Predicted nucleic-acid 30.8 11 0.00023 29.0 -1.0 35 163-197 9-43 (66)
36 PF10083 DUF2321: Uncharacteri 29.9 28 0.00061 30.9 1.3 34 164-197 39-79 (158)
37 PF12773 DZR: Double zinc ribb 29.6 29 0.00064 23.6 1.1 30 163-197 11-40 (50)
38 PRK00420 hypothetical protein; 29.3 28 0.0006 29.1 1.1 30 163-197 22-51 (112)
39 PRK00241 nudC NADH pyrophospha 29.0 24 0.00052 32.5 0.7 31 163-197 98-128 (256)
40 PF04810 zf-Sec23_Sec24: Sec23 28.5 27 0.00059 23.5 0.8 33 165-197 3-35 (40)
41 TIGR01385 TFSII transcription 26.7 31 0.00068 32.9 1.1 36 162-197 256-297 (299)
42 PHA02998 RNA polymerase subuni 26.3 36 0.00078 31.1 1.3 34 164-197 143-182 (195)
43 COG4888 Uncharacterized Zn rib 26.2 33 0.00072 28.5 1.0 45 165-214 23-69 (104)
44 PRK00423 tfb transcription ini 24.7 38 0.00082 31.9 1.3 31 164-197 11-41 (310)
45 TIGR00244 transcriptional regu 24.5 43 0.00092 29.3 1.4 33 166-198 2-40 (147)
46 PF09526 DUF2387: Probable met 24.5 25 0.00055 27.0 0.0 35 163-197 7-41 (71)
47 smart00440 ZnF_C2C2 C2C2 Zinc 24.3 28 0.00061 23.6 0.2 32 166-197 2-39 (40)
48 PF11781 RRN7: RNA polymerase 24.1 40 0.00087 22.6 0.9 26 164-194 8-33 (36)
49 PRK00464 nrdR transcriptional 23.0 42 0.0009 29.2 1.1 32 166-197 2-39 (154)
50 PRK13130 H/ACA RNA-protein com 22.9 58 0.0013 24.1 1.7 24 164-197 5-28 (56)
51 KOG1598 Transcription initiati 21.8 51 0.0011 34.2 1.6 31 165-198 1-31 (521)
52 PF09723 Zn-ribbon_8: Zinc rib 21.7 34 0.00075 23.2 0.3 28 166-194 7-34 (42)
53 PRK00085 recO DNA repair prote 20.9 49 0.0011 29.2 1.1 28 165-193 150-177 (247)
54 smart00778 Prim_Zn_Ribbon Zinc 20.8 69 0.0015 21.8 1.6 29 165-194 4-33 (37)
55 PF05876 Terminase_GpA: Phage 20.5 51 0.0011 33.7 1.3 33 165-197 201-240 (557)
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=99.52 E-value=5.1e-15 Score=106.94 Aligned_cols=44 Identities=45% Similarity=0.974 Sum_probs=39.4
Q ss_pred ccccCCCCCCCccccCCCCCccccchhhhhhhcCCCCCCCCCCCCCC
Q 024757 166 RCTHCASEKTPQWRTGPLGPKTLCNACGVRYKSGRLVPEYRPASSPT 212 (263)
Q Consensus 166 ~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk~grl~p~~RP~~spt 212 (263)
.|+||++++||+||+||.|..+|||||||||++. ...||+..+.
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 4999999999999999988899999999999954 4778887766
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.50 E-value=1.4e-14 Score=103.63 Aligned_cols=47 Identities=49% Similarity=0.960 Sum_probs=39.0
Q ss_pred CCcccccCCCCCCCccccCCCCCccccchhhhhhhcCCCCCCCCCCCCC
Q 024757 163 GVRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYKSGRLVPEYRPASSP 211 (263)
Q Consensus 163 ~~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk~grl~p~~RP~~sp 211 (263)
..+.|+||+++.||+||+||.|...|||||||||++.+.. +||+...
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~--~rp~~~~ 48 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL--KRPLSLK 48 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC--CCccccc
Confidence 4578999999999999999999889999999999974332 4665544
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=99.38 E-value=6.3e-14 Score=93.50 Aligned_cols=34 Identities=56% Similarity=1.256 Sum_probs=27.0
Q ss_pred cccCCCCCCCccccCCCCCccccchhhhhhhcCC
Q 024757 167 CTHCASEKTPQWRTGPLGPKTLCNACGVRYKSGR 200 (263)
Q Consensus 167 C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk~gr 200 (263)
|.||++++||+||+||.|..+||||||++|++.+
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 8999999999999999998889999999999743
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.99 E-value=3.2e-10 Score=95.04 Aligned_cols=49 Identities=65% Similarity=1.359 Sum_probs=43.7
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhhhhhcC---CCCCCCCCCCCCC
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYKSG---RLVPEYRPASSPT 212 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk~g---rl~p~~RP~~spt 212 (263)
...|.+|++..||+||+++.|++.+|||||++|+++ +.++.++....+.
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 6777777766655
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.37 E-value=1.6e-07 Score=93.39 Aligned_cols=54 Identities=33% Similarity=0.623 Sum_probs=48.3
Q ss_pred CCcccccCCCCCCCccccCCCC----CccccchhhhhhhcCCCCCCCC-CCCCCCccccccc
Q 024757 163 GVRRCTHCASEKTPQWRTGPLG----PKTLCNACGVRYKSGRLVPEYR-PASSPTFVLTQHS 219 (263)
Q Consensus 163 ~~r~C~~Cgt~~TP~WRrGP~G----~~~LCNACGl~yk~grl~p~~R-P~~spt~~~~~hs 219 (263)
....|.||.+..||+|||+..+ .-+|||||||+|+ +|...| |+.+++.++..|.
T Consensus 157 ~~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~k---lhg~~r~P~t~ks~~~ks~~ 215 (498)
T COG5641 157 QPHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLK---LHGSPRAPISLKSDSIKSRS 215 (498)
T ss_pred ccchhccccccCCccccccccccccCCcccccccccccc---ccCCcCCCcccccccccccc
Confidence 3458999999999999999993 3899999999999 899999 9999999988776
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=89.88 E-value=0.17 Score=51.49 Aligned_cols=39 Identities=31% Similarity=0.651 Sum_probs=32.9
Q ss_pred CCcccccCCCCCCCcc--ccCCCCCccccchhhhhhhc-CCC
Q 024757 163 GVRRCTHCASEKTPQW--RTGPLGPKTLCNACGVRYKS-GRL 201 (263)
Q Consensus 163 ~~r~C~~Cgt~~TP~W--RrGP~G~~~LCNACGl~yk~-grl 201 (263)
.++.|-+|++++.-+| .-+|+..+.||-.|-+|||| |+|
T Consensus 385 ~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 385 DGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred CCCcccccccccccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 4689999999999999 55666667899999999998 444
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=86.94 E-value=0.42 Score=48.48 Aligned_cols=43 Identities=26% Similarity=0.363 Sum_probs=33.3
Q ss_pred CcccccCCC-CCCCccccCCCCCccccchhhhhhhcCCCCCCCCCCC
Q 024757 164 VRRCTHCAS-EKTPQWRTGPLGPKTLCNACGVRYKSGRLVPEYRPAS 209 (263)
Q Consensus 164 ~r~C~~Cgt-~~TP~WRrGP~G~~~LCNACGl~yk~grl~p~~RP~~ 209 (263)
...|.+|++ +.||.||+...-.-++|||||++.+ +...++|+.
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~---~~~~~~p~~ 340 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALK---PPGSKRPLL 340 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccC---CcccccccC
Confidence 457888887 7899999988777999999999998 444444443
No 8
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=72.97 E-value=2.4 Score=34.49 Aligned_cols=34 Identities=15% Similarity=0.293 Sum_probs=22.7
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhhhhhc
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYKS 198 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk~ 198 (263)
.-.|.+|+...-+.=+. -...+..|..||.|+..
T Consensus 21 ~f~CP~Cge~~v~v~~~-k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 21 IFECPRCGKVSISVKIK-KNIAIITCGNCGLYTEF 54 (99)
T ss_pred EeECCCCCCeEeeeecC-CCcceEECCCCCCccCE
Confidence 35799999543332222 23458999999999874
No 9
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=72.75 E-value=1.1 Score=29.94 Aligned_cols=30 Identities=23% Similarity=0.607 Sum_probs=15.8
Q ss_pred cccccCCCCCCCccccCCCCCccccchhhh
Q 024757 165 RRCTHCASEKTPQWRTGPLGPKTLCNACGV 194 (263)
Q Consensus 165 r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl 194 (263)
+.|.+||..-+-.--.|..-.+.+|.+||.
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 469999987543333566666789999984
No 10
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=65.17 E-value=2.2 Score=36.41 Aligned_cols=32 Identities=28% Similarity=0.550 Sum_probs=24.5
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhhhh
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGVRY 196 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~y 196 (263)
-..|..|+.+.|-.=+.+-.- -..|+|||-..
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 368999999999998753322 46899999653
No 11
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=63.06 E-value=2.6 Score=35.81 Aligned_cols=32 Identities=25% Similarity=0.559 Sum_probs=24.1
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhhhh
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGVRY 196 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~y 196 (263)
-..|..|+.+.|-.-+.+..- -.-|+|||-..
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 367999999999988753321 35899999654
No 12
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=62.61 E-value=5.3 Score=29.43 Aligned_cols=24 Identities=29% Similarity=0.850 Sum_probs=19.1
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhhhh
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGVRY 196 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~y 196 (263)
.-.|.+||...-| +.+|..||.|-
T Consensus 27 l~~C~~CG~~~~~---------H~vC~~CG~Y~ 50 (57)
T PRK12286 27 LVECPNCGEPKLP---------HRVCPSCGYYK 50 (57)
T ss_pred ceECCCCCCccCC---------eEECCCCCcCC
Confidence 4579999987655 88999999554
No 13
>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=61.54 E-value=4.3 Score=29.43 Aligned_cols=25 Identities=36% Similarity=0.999 Sum_probs=18.5
Q ss_pred CCcccccCCCCCCCccccCCCCCccccchhhhhhh
Q 024757 163 GVRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYK 197 (263)
Q Consensus 163 ~~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk 197 (263)
....|.+||... -++.+|.+|| +|+
T Consensus 25 ~l~~c~~cg~~~---------~~H~vc~~cG-~y~ 49 (56)
T PF01783_consen 25 NLVKCPNCGEPK---------LPHRVCPSCG-YYK 49 (56)
T ss_dssp SEEESSSSSSEE---------STTSBCTTTB-BSS
T ss_pred ceeeeccCCCEe---------cccEeeCCCC-eEC
Confidence 346899999643 3488999999 555
No 14
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=60.71 E-value=3 Score=34.33 Aligned_cols=29 Identities=31% Similarity=0.550 Sum_probs=22.7
Q ss_pred cccccCCCCCCCccccCCCCCccccchhhh
Q 024757 165 RRCTHCASEKTPQWRTGPLGPKTLCNACGV 194 (263)
Q Consensus 165 r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl 194 (263)
..|..|+.+.|-+=+.+..- -.-|+|||-
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 15
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=57.55 E-value=3.6 Score=36.79 Aligned_cols=33 Identities=21% Similarity=0.425 Sum_probs=25.4
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhhhhh
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYK 197 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk 197 (263)
--.|..|+.+.|-+=+.+..- -.-|+|||-..-
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 368999999999998764222 458999998764
No 16
>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=56.08 E-value=9.8 Score=30.67 Aligned_cols=49 Identities=27% Similarity=0.597 Sum_probs=37.5
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhhhhhc-CCCCCCCCCCCCCCcc
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYKS-GRLVPEYRPASSPTFV 214 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk~-grl~p~~RP~~spt~~ 214 (263)
.+.|..|+. .-|+|-.=..| -.||-.|.-..+. |.-+...+.+.+.++.
T Consensus 3 N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~lg~his~VkSl~md~w~ 52 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRSLGVHISKVRSLTLDTWT 52 (112)
T ss_pred CCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHhcCCCcCeeeecccCCCC
Confidence 478999998 55999988889 8999999888875 3333456777776554
No 17
>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=50.27 E-value=6 Score=26.83 Aligned_cols=30 Identities=23% Similarity=0.725 Sum_probs=19.1
Q ss_pred ccccCCCCCCCccccCCCCCccccchhhhhhhc
Q 024757 166 RCTHCASEKTPQWRTGPLGPKTLCNACGVRYKS 198 (263)
Q Consensus 166 ~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk~ 198 (263)
.|.+|++.. -.+ .--.| ..+|..||+-..-
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 589999866 222 23344 7899999987653
No 18
>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=47.84 E-value=5.8 Score=33.28 Aligned_cols=29 Identities=34% Similarity=0.628 Sum_probs=23.8
Q ss_pred cccccCCCCCCCccccCCCCCccccchhhh
Q 024757 165 RRCTHCASEKTPQWRTGPLGPKTLCNACGV 194 (263)
Q Consensus 165 r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl 194 (263)
..|..|+.+.|-+=+.+..- -.-|+|||-
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 57999999999998874444 678999995
No 19
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=44.04 E-value=12 Score=38.20 Aligned_cols=33 Identities=24% Similarity=0.550 Sum_probs=23.4
Q ss_pred cccccCCCCC-CCccccCCCCCc----------cccchhhhhhh
Q 024757 165 RRCTHCASEK-TPQWRTGPLGPK----------TLCNACGVRYK 197 (263)
Q Consensus 165 r~C~~Cgt~~-TP~WRrGP~G~~----------~LCNACGl~yk 197 (263)
-.|.+||... ++.=+-+|.+.. +.||+||---+
T Consensus 162 PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~R 205 (500)
T KOG0909|consen 162 PPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETR 205 (500)
T ss_pred CCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCccc
Confidence 4699999877 555554554432 79999998766
No 20
>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=43.79 E-value=15 Score=30.29 Aligned_cols=14 Identities=36% Similarity=1.047 Sum_probs=6.4
Q ss_pred CCccccchhhhhhh
Q 024757 184 GPKTLCNACGVRYK 197 (263)
Q Consensus 184 G~~~LCNACGl~yk 197 (263)
|.+.+|..||.+|-
T Consensus 7 GtKR~Cp~CG~kFY 20 (108)
T PF09538_consen 7 GTKRTCPSCGAKFY 20 (108)
T ss_pred CCcccCCCCcchhc
Confidence 33444444444443
No 21
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.75 E-value=9.8 Score=40.16 Aligned_cols=37 Identities=19% Similarity=0.567 Sum_probs=30.3
Q ss_pred CCCcccccCCCCCCCccccCCCC---Cccccchhhhhhhc
Q 024757 162 GGVRRCTHCASEKTPQWRTGPLG---PKTLCNACGVRYKS 198 (263)
Q Consensus 162 ~~~r~C~~Cgt~~TP~WRrGP~G---~~~LCNACGl~yk~ 198 (263)
++.-.|..|.+.-||.|+.-+.+ .+.+|.+|-.--.+
T Consensus 460 ~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSnqk 499 (706)
T KOG3740|consen 460 TEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSNQK 499 (706)
T ss_pred CCchhhhhcccccccccccccccCcchHHHHHhhhhhccc
Confidence 45678999999999999987777 46799999765554
No 22
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=43.03 E-value=12 Score=36.20 Aligned_cols=35 Identities=29% Similarity=0.732 Sum_probs=30.2
Q ss_pred CCCcccccCCCCCCCccccCCCCCccccchhhhhhhc
Q 024757 162 GGVRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYKS 198 (263)
Q Consensus 162 ~~~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk~ 198 (263)
...+.|..|+... |+|-.=..| -.||--|.--.+.
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 3458899999999 999999999 9999999766654
No 23
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=42.97 E-value=16 Score=27.14 Aligned_cols=24 Identities=8% Similarity=-0.003 Sum_probs=17.7
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhhhhh
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYK 197 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk 197 (263)
...|.+||...-| +.+|. ||.|.-
T Consensus 27 ~~~c~~cg~~~~p---------H~vc~-cG~Y~g 50 (60)
T PRK01110 27 LSVDKTTGEYHLP---------HHVSP-KGYYKG 50 (60)
T ss_pred eeEcCCCCceecc---------ceecC-CcccCC
Confidence 3579999986654 67899 996543
No 24
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=41.77 E-value=14 Score=29.97 Aligned_cols=48 Identities=23% Similarity=0.555 Sum_probs=29.3
Q ss_pred CCcccccCCCCCCCccccCCCCCccccchhhhhhhc-CCCCCCCCCCCCCC
Q 024757 163 GVRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYKS-GRLVPEYRPASSPT 212 (263)
Q Consensus 163 ~~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk~-grl~p~~RP~~spt 212 (263)
+.+.|..|+... |.|-.=..| -.||-.|.-..+. |..+-..+.+.+.+
T Consensus 12 ~N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~lg~~is~VkSi~~d~ 60 (116)
T PF01412_consen 12 GNKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRSLGVHISRVKSITMDN 60 (116)
T ss_dssp TCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHHHTTTT--EEETTTS-
T ss_pred CcCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHHhcccchhccccccCC
Confidence 457999999554 699998899 9999999988875 44333444554443
No 25
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=41.21 E-value=22 Score=35.45 Aligned_cols=49 Identities=22% Similarity=0.539 Sum_probs=37.1
Q ss_pred CCcccccCCCCCCCccccCCCCCccccchhhhhhhc-CCCCCCCCCCCCCCc
Q 024757 163 GVRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYKS-GRLVPEYRPASSPTF 213 (263)
Q Consensus 163 ~~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk~-grl~p~~RP~~spt~ 213 (263)
+.++|..|+... |.|-.=..| -.||-.|.-..+. |..+...|.+.+.++
T Consensus 21 gNk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRsLGvHISfVRSltLD~W 70 (395)
T PLN03114 21 DNKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRSLGVHISFVRSTNLDSW 70 (395)
T ss_pred CCCcCccCCCCC-CCceeeccc-eeehhhhhHhhccCCCCCceeecccCCCC
Confidence 457899999865 999999999 9999999877765 444445666666543
No 26
>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=39.75 E-value=13 Score=26.95 Aligned_cols=31 Identities=19% Similarity=0.534 Sum_probs=23.0
Q ss_pred CCcccccCCCCCCCccccCCCCCccccchhhhhhh
Q 024757 163 GVRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYK 197 (263)
Q Consensus 163 ~~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk 197 (263)
....|..||....- ...+....|..||..+.
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 45789999986654 44555789999998765
No 27
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=39.54 E-value=18 Score=22.30 Aligned_cols=23 Identities=30% Similarity=0.925 Sum_probs=14.5
Q ss_pred cccccCCCCCCCccccCCCCCccccchhhhh
Q 024757 165 RRCTHCASEKTPQWRTGPLGPKTLCNACGVR 195 (263)
Q Consensus 165 r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~ 195 (263)
+.|.+||....+. ...|-.||..
T Consensus 3 ~~Cp~Cg~~~~~~--------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPD--------AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcc--------cccChhhCCC
Confidence 5688888754332 4477777753
No 28
>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=37.92 E-value=18 Score=24.88 Aligned_cols=28 Identities=29% Similarity=0.503 Sum_probs=19.9
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhh
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGV 194 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl 194 (263)
+-.|.+||.+ ..-|.++ .+ ...|++|+-
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 3569999998 4545444 34 789999974
No 29
>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=37.39 E-value=23 Score=25.84 Aligned_cols=23 Identities=30% Similarity=0.833 Sum_probs=17.4
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhhh
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGVR 195 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~ 195 (263)
.-.|.+||...- ++.+|-.||.|
T Consensus 26 l~~C~~cG~~~~---------~H~vc~~cG~Y 48 (55)
T TIGR01031 26 LVVCPNCGEFKL---------PHRVCPSCGYY 48 (55)
T ss_pred ceECCCCCCccc---------CeeECCccCeE
Confidence 457999997543 38899999943
No 30
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=37.33 E-value=17 Score=34.75 Aligned_cols=30 Identities=27% Similarity=0.574 Sum_probs=23.4
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhhhhh
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYK 197 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk 197 (263)
-|.|.+||+...+. ..|-+.+|+.||.++-
T Consensus 111 ~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~f 140 (279)
T COG2816 111 HRFCGRCGTKTYPR----EGGWARVCPKCGHEHF 140 (279)
T ss_pred CcCCCCCCCcCccc----cCceeeeCCCCCCccC
Confidence 47899999988764 2445789999998875
No 31
>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=37.17 E-value=7.6 Score=24.87 Aligned_cols=29 Identities=28% Similarity=0.531 Sum_probs=15.8
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhhhh
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGVRY 196 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~y 196 (263)
.+.|..||....+.. .|....|.+||..+
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 367999998765542 34567899998754
No 32
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=36.95 E-value=7.7 Score=26.19 Aligned_cols=32 Identities=22% Similarity=0.640 Sum_probs=19.7
Q ss_pred ccccCCCCCCCcc----ccCCCCC--ccccchhhhhhh
Q 024757 166 RCTHCASEKTPQW----RTGPLGP--KTLCNACGVRYK 197 (263)
Q Consensus 166 ~C~~Cgt~~TP~W----RrGP~G~--~~LCNACGl~yk 197 (263)
.|..||...+--| |.+.++. -+.|..||-+|+
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 5888988764443 6666663 258999998774
No 33
>PF05361 PP1_inhibitor: PKC-activated protein phosphatase-1 inhibitor; InterPro: IPR008025 Contractility of vascular smooth muscle depends on phosphorylation of myosin light chains, and is modulated by hormonal control of myosin phosphatase activity. Signaling pathways activate kinases such as PKC or Rho-dependent kinases that phosphorylate the myosin phosphatase inhibitor protein called CPI-17. Phosphorylation of CPI-17 at Thr-38 enhances its inhibitory potency 1000-fold, creating a molecular switch for regulating contraction [].; GO: 0042325 regulation of phosphorylation, 0005737 cytoplasm; PDB: 2RLT_A 1J2M_A 1K5O_A 1J2N_A.
Probab=35.10 E-value=17 Score=31.78 Aligned_cols=25 Identities=32% Similarity=0.635 Sum_probs=17.9
Q ss_pred ccCCCCCCCCCCCccccccccCCCCcc
Q 024757 3 IYGLPSNNTTTQDLFRIDDLLDFSNDE 29 (263)
Q Consensus 3 ~~~~~~~~~~~~d~f~vdDLLdfsn~d 29 (263)
+|.-.... .++++-||||||+++++
T Consensus 62 Ly~~~e~~--~p~EIDIDeLLDl~sde 86 (144)
T PF05361_consen 62 LYDCQEDE--MPEEIDIDELLDLESDE 86 (144)
T ss_dssp CSSSSSTT--S-SSSHHHHHHCTSSTT
T ss_pred HhcCCCCC--CCCcccHHHHhcCCchH
Confidence 45544433 45689999999999987
No 34
>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=31.30 E-value=24 Score=24.54 Aligned_cols=25 Identities=40% Similarity=0.878 Sum_probs=19.2
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhh
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACG 193 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACG 193 (263)
...|..| .+|+.| ...| ..+|-+|+
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 4578889 489999 3356 78999996
No 35
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=30.85 E-value=11 Score=28.95 Aligned_cols=35 Identities=17% Similarity=0.305 Sum_probs=26.5
Q ss_pred CCcccccCCCCCCCccccCCCCCccccchhhhhhh
Q 024757 163 GVRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYK 197 (263)
Q Consensus 163 ~~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk 197 (263)
.+..|..|.+..|-+|.+-..-...-|.+||-.-+
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 34679999999987754444444889999997764
No 36
>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=29.87 E-value=28 Score=30.85 Aligned_cols=34 Identities=21% Similarity=0.704 Sum_probs=24.5
Q ss_pred CcccccCCCCCCCcccc-------CCCCCccccchhhhhhh
Q 024757 164 VRRCTHCASEKTPQWRT-------GPLGPKTLCNACGVRYK 197 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRr-------GP~G~~~LCNACGl~yk 197 (263)
...|.+|++..--.|-- ++......|+.||..|-
T Consensus 39 I~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyP 79 (158)
T PF10083_consen 39 ITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYP 79 (158)
T ss_pred HHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCc
Confidence 36799998877655532 44555679999999883
No 37
>PF12773 DZR: Double zinc ribbon
Probab=29.64 E-value=29 Score=23.60 Aligned_cols=30 Identities=27% Similarity=0.697 Sum_probs=20.6
Q ss_pred CCcccccCCCCCCCccccCCCCCccccchhhhhhh
Q 024757 163 GVRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYK 197 (263)
Q Consensus 163 ~~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk 197 (263)
..+.|.+||+.-. ........|..||-.+.
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGAENP 40 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcCCCc
Confidence 4578888888776 33343568888887654
No 38
>PRK00420 hypothetical protein; Validated
Probab=29.34 E-value=28 Score=29.06 Aligned_cols=30 Identities=23% Similarity=0.555 Sum_probs=23.2
Q ss_pred CCcccccCCCCCCCccccCCCCCccccchhhhhhh
Q 024757 163 GVRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYK 197 (263)
Q Consensus 163 ~~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk 197 (263)
....|..|| +|..|- ..| ...|-+||..+.
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 346799998 677774 355 889999999776
No 39
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=28.95 E-value=24 Score=32.52 Aligned_cols=31 Identities=29% Similarity=0.534 Sum_probs=22.0
Q ss_pred CCcccccCCCCCCCccccCCCCCccccchhhhhhh
Q 024757 163 GVRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYK 197 (263)
Q Consensus 163 ~~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk 197 (263)
..+.|.+||...... ..|....|.+||..+-
T Consensus 98 ~~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 98 SHRFCGYCGHPMHPS----KTEWAMLCPHCRERYY 128 (256)
T ss_pred cCccccccCCCCeec----CCceeEECCCCCCEEC
Confidence 357899999875542 3455678999997654
No 40
>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=28.47 E-value=27 Score=23.54 Aligned_cols=33 Identities=27% Similarity=0.584 Sum_probs=20.9
Q ss_pred cccccCCCCCCCccccCCCCCccccchhhhhhh
Q 024757 165 RRCTHCASEKTPQWRTGPLGPKTLCNACGVRYK 197 (263)
Q Consensus 165 r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk 197 (263)
-+|.+|++---|.=.-...|..-.||-|+..-.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~ 35 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNP 35 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--EEE
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCCcCC
Confidence 579999999988877777777789999997543
No 41
>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=26.73 E-value=31 Score=32.89 Aligned_cols=36 Identities=25% Similarity=0.588 Sum_probs=25.5
Q ss_pred CCCcccccCCCCCCCcc----ccCCCC--Cccccchhhhhhh
Q 024757 162 GGVRRCTHCASEKTPQW----RTGPLG--PKTLCNACGVRYK 197 (263)
Q Consensus 162 ~~~r~C~~Cgt~~TP~W----RrGP~G--~~~LCNACGl~yk 197 (263)
+....|..|+-...--| |...++ --+.|..||-+|+
T Consensus 256 t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 256 TDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 45689999997776555 443333 1259999999987
No 42
>PHA02998 RNA polymerase subunit; Provisional
Probab=26.28 E-value=36 Score=31.06 Aligned_cols=34 Identities=26% Similarity=0.589 Sum_probs=27.0
Q ss_pred CcccccCCCCCCCcc----ccCCCCCc--cccchhhhhhh
Q 024757 164 VRRCTHCASEKTPQW----RTGPLGPK--TLCNACGVRYK 197 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~W----RrGP~G~~--~LCNACGl~yk 197 (263)
...|..|+-..+--| |.+.++.- +.|-.||-+|+
T Consensus 143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccC
Confidence 468999998887755 77776632 49999999998
No 43
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=26.23 E-value=33 Score=28.54 Aligned_cols=45 Identities=24% Similarity=0.484 Sum_probs=28.9
Q ss_pred cccccCCCCCCCc--cccCCCCCccccchhhhhhhcCCCCCCCCCCCCCCcc
Q 024757 165 RRCTHCASEKTPQ--WRTGPLGPKTLCNACGVRYKSGRLVPEYRPASSPTFV 214 (263)
Q Consensus 165 r~C~~Cgt~~TP~--WRrGP~G~~~LCNACGl~yk~grl~p~~RP~~spt~~ 214 (263)
-.|.+|+..+..+ -.++-...-..|-.||+++.- +.+++.+|-++
T Consensus 23 FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~-----ev~~l~~~vDv 69 (104)
T COG4888 23 FTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFEC-----EVPELSEPVDV 69 (104)
T ss_pred EecCccCCeeeeEEEEEecCceeEEEcccCcceEEE-----eccccccchhH
Confidence 5699999766442 344444436799999999983 23445555443
No 44
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=24.74 E-value=38 Score=31.86 Aligned_cols=31 Identities=23% Similarity=0.496 Sum_probs=16.1
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhhhhh
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYK 197 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk 197 (263)
...|.+||. +..--.--.| .++|..||+=..
T Consensus 11 ~~~Cp~Cg~--~~iv~d~~~G-e~vC~~CG~Vl~ 41 (310)
T PRK00423 11 KLVCPECGS--DKLIYDYERG-EIVCADCGLVIE 41 (310)
T ss_pred CCcCcCCCC--CCeeEECCCC-eEeecccCCccc
Confidence 345777774 2222222345 667777776443
No 45
>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=24.53 E-value=43 Score=29.35 Aligned_cols=33 Identities=24% Similarity=0.542 Sum_probs=25.1
Q ss_pred ccccCCCCCCCcc--ccCCCCC----ccccchhhhhhhc
Q 024757 166 RCTHCASEKTPQW--RTGPLGP----KTLCNACGVRYKS 198 (263)
Q Consensus 166 ~C~~Cgt~~TP~W--RrGP~G~----~~LCNACGl~yk~ 198 (263)
+|..|+...|-.- |....|. .-.|.+||-+|-.
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTT 40 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTT 40 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccce
Confidence 6999999888876 5455552 3689999999863
No 46
>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=24.46 E-value=25 Score=26.99 Aligned_cols=35 Identities=17% Similarity=0.241 Sum_probs=27.2
Q ss_pred CCcccccCCCCCCCccccCCCCCccccchhhhhhh
Q 024757 163 GVRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYK 197 (263)
Q Consensus 163 ~~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk 197 (263)
.+-.|-.|....|-+|.+.......-|-+||-.-.
T Consensus 7 AGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 7 AGAVCPKCQAMDTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred cCccCCCCcCccEEEEEEeCCceEEEecCCCCeec
Confidence 34689999999988765444455889999998776
No 47
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=24.27 E-value=28 Score=23.60 Aligned_cols=32 Identities=22% Similarity=0.651 Sum_probs=21.2
Q ss_pred ccccCCCCCCCcc----ccCCCCC--ccccchhhhhhh
Q 024757 166 RCTHCASEKTPQW----RTGPLGP--KTLCNACGVRYK 197 (263)
Q Consensus 166 ~C~~Cgt~~TP~W----RrGP~G~--~~LCNACGl~yk 197 (263)
.|.+|+-...--| |...++. -+.|-.||-+|+
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 5888886664433 5555553 258999998775
No 48
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=24.05 E-value=40 Score=22.63 Aligned_cols=26 Identities=31% Similarity=0.729 Sum_probs=19.7
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhh
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGV 194 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl 194 (263)
...|..|+.. |-...+| .+.|..||-
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 3459999887 5556677 889999985
No 49
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=23.01 E-value=42 Score=29.25 Aligned_cols=32 Identities=31% Similarity=0.673 Sum_probs=21.9
Q ss_pred ccccCCCCCCCccccC--CCC----Cccccchhhhhhh
Q 024757 166 RCTHCASEKTPQWRTG--PLG----PKTLCNACGVRYK 197 (263)
Q Consensus 166 ~C~~Cgt~~TP~WRrG--P~G----~~~LCNACGl~yk 197 (263)
.|.+||...|-.--.- +.| ...-|.+||-++.
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~ 39 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFT 39 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcce
Confidence 6999998887653221 122 2378999999886
No 50
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=22.90 E-value=58 Score=24.14 Aligned_cols=24 Identities=33% Similarity=0.905 Sum_probs=17.0
Q ss_pred CcccccCCCCCCCccccCCCCCccccchhhhhhh
Q 024757 164 VRRCTHCASEKTPQWRTGPLGPKTLCNACGVRYK 197 (263)
Q Consensus 164 ~r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk 197 (263)
.+.|..||+-.- +..|-.||....
T Consensus 5 mr~C~~CgvYTL----------k~~CP~CG~~t~ 28 (56)
T PRK13130 5 IRKCPKCGVYTL----------KEICPVCGGKTK 28 (56)
T ss_pred ceECCCCCCEEc----------cccCcCCCCCCC
Confidence 467888887655 457888886654
No 51
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=21.85 E-value=51 Score=34.16 Aligned_cols=31 Identities=26% Similarity=0.637 Sum_probs=21.3
Q ss_pred cccccCCCCCCCccccCCCCCccccchhhhhhhc
Q 024757 165 RRCTHCASEKTPQWRTGPLGPKTLCNACGVRYKS 198 (263)
Q Consensus 165 r~C~~Cgt~~TP~WRrGP~G~~~LCNACGl~yk~ 198 (263)
+.|.||+.+. +. |+--.| ...|.+||.-..-
T Consensus 1 ~~C~~C~~s~-fe-~d~a~g-~~~C~~CG~v~E~ 31 (521)
T KOG1598|consen 1 MVCKNCGGSN-FE-RDEATG-NLYCTACGTVLEY 31 (521)
T ss_pred CcCCCCCCCC-cc-cccccC-Cceeccccceeec
Confidence 3699999754 21 222455 8899999987653
No 52
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.73 E-value=34 Score=23.22 Aligned_cols=28 Identities=25% Similarity=0.545 Sum_probs=16.4
Q ss_pred ccccCCCCCCCccccCCCCCccccchhhh
Q 024757 166 RCTHCASEKTPQWRTGPLGPKTLCNACGV 194 (263)
Q Consensus 166 ~C~~Cgt~~TP~WRrGP~G~~~LCNACGl 194 (263)
+|..||..-+-...-.. .....|-+||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 57777755544333222 44667888876
No 53
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=20.91 E-value=49 Score=29.19 Aligned_cols=28 Identities=21% Similarity=0.692 Sum_probs=23.6
Q ss_pred cccccCCCCCCCccccCCCCCccccchhh
Q 024757 165 RRCTHCASEKTPQWRTGPLGPKTLCNACG 193 (263)
Q Consensus 165 r~C~~Cgt~~TP~WRrGP~G~~~LCNACG 193 (263)
..|..||......|-.-..| ..+|..|+
T Consensus 150 ~~C~~Cg~~~~~~~f~~~~g-g~~c~~c~ 177 (247)
T PRK00085 150 DHCAVCGAPGDHRYFSPKEG-GAVCSECG 177 (247)
T ss_pred hhHhcCCCCCCceEEecccC-Cccccccc
Confidence 57999998877677777777 99999997
No 54
>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=20.84 E-value=69 Score=21.83 Aligned_cols=29 Identities=21% Similarity=0.642 Sum_probs=19.7
Q ss_pred cccccCCCCCCCccccC-CCCCccccchhhh
Q 024757 165 RRCTHCASEKTPQWRTG-PLGPKTLCNACGV 194 (263)
Q Consensus 165 r~C~~Cgt~~TP~WRrG-P~G~~~LCNACGl 194 (263)
..|-.|+....=.|..- ..| ...|+.||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G-~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRG-TWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCc-CEEeCCCCC
Confidence 46889988766556442 234 679999974
No 55
>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=20.53 E-value=51 Score=33.71 Aligned_cols=33 Identities=30% Similarity=0.893 Sum_probs=26.4
Q ss_pred cccccCCCCCCCcccc-----C--CCCCccccchhhhhhh
Q 024757 165 RRCTHCASEKTPQWRT-----G--PLGPKTLCNACGVRYK 197 (263)
Q Consensus 165 r~C~~Cgt~~TP~WRr-----G--P~G~~~LCNACGl~yk 197 (263)
..|-|||......|.. | +....+.|-.||-.+.
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCC
Confidence 6899999999988743 2 4455789999998875
Done!