Query 030971
Match_columns 168
No_of_seqs 161 out of 794
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 07:19:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030971.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030971hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00401 ZnF_GATA zinc finge 99.5 8.1E-15 1.7E-19 98.5 3.1 46 7-52 2-47 (52)
2 cd00202 ZnF_GATA Zinc finger D 99.5 9.1E-15 2E-19 99.2 3.2 43 10-53 1-43 (54)
3 PF00320 GATA: GATA zinc finge 99.4 2.4E-14 5.3E-19 89.7 1.3 34 11-44 1-34 (36)
4 KOG1601 GATA-4/5/6 transcripti 98.7 7.2E-09 1.6E-13 81.4 2.7 44 8-52 199-242 (340)
5 COG5641 GAT1 GATA Zn-finger-co 98.2 4.5E-07 9.8E-12 84.6 0.9 44 9-54 159-208 (498)
6 KOG3554 Histone deacetylase co 93.6 0.061 1.3E-06 51.3 3.2 40 6-45 384-425 (693)
7 COG5641 GAT1 GATA Zn-finger-co 82.5 0.74 1.6E-05 43.7 1.7 44 8-52 297-341 (498)
8 PF14803 Nudix_N_2: Nudix N-te 77.9 0.55 1.2E-05 29.3 -0.5 30 9-38 1-30 (34)
9 PF15396 FAM60A: Protein Famil 77.7 0.79 1.7E-05 39.3 0.2 20 30-49 49-68 (213)
10 PF01412 ArfGap: Putative GTPa 72.2 3.7 7.9E-05 31.0 2.6 38 5-44 10-47 (116)
11 smart00653 eIF2B_5 domain pres 69.5 1.5 3.2E-05 33.7 -0.1 29 9-38 81-109 (110)
12 COG5347 GTPase-activating prot 65.6 2.8 6E-05 37.7 0.9 30 5-36 17-46 (319)
13 PRK12336 translation initiatio 65.3 1.8 4E-05 36.0 -0.3 30 8-38 98-127 (201)
14 smart00105 ArfGap Putative GTP 59.5 7.9 0.00017 29.1 2.3 35 7-43 2-36 (112)
15 PF09889 DUF2116: Uncharacteri 59.4 8.4 0.00018 26.8 2.2 31 7-45 2-33 (59)
16 KOG3740 Uncharacterized conser 59.2 4.2 9.1E-05 40.1 0.9 37 6-42 460-499 (706)
17 PF08271 TF_Zn_Ribbon: TFIIB z 57.9 3.5 7.6E-05 26.0 0.1 26 10-38 2-27 (43)
18 PF12773 DZR: Double zinc ribb 53.4 8 0.00017 24.6 1.2 32 2-38 6-37 (50)
19 PF11781 RRN7: RNA polymerase 53.2 7 0.00015 24.4 0.9 28 6-38 6-33 (36)
20 PLN03114 ADP-ribosylation fact 51.9 8 0.00017 35.9 1.4 32 5-38 19-50 (395)
21 PF13248 zf-ribbon_3: zinc-rib 50.1 11 0.00023 21.7 1.3 23 8-38 2-24 (26)
22 PF01783 Ribosomal_L32p: Ribos 46.1 3.5 7.6E-05 27.8 -1.4 22 7-37 25-46 (56)
23 KOG0703 Predicted GTPase-activ 46.0 8.9 0.00019 34.3 0.7 28 7-36 24-51 (287)
24 PF06677 Auto_anti-p27: Sjogre 45.2 7.8 0.00017 25.1 0.2 25 8-37 17-41 (41)
25 PRK00423 tfb transcription ini 44.8 9 0.00019 33.6 0.6 33 5-40 8-40 (310)
26 PF09297 zf-NADH-PPase: NADH p 44.0 2.1 4.7E-05 25.5 -2.4 28 8-39 3-30 (32)
27 COG3529 Predicted nucleic-acid 43.7 4.7 0.0001 28.8 -1.1 33 8-40 10-42 (66)
28 COG2816 NPY1 NTP pyrophosphohy 43.2 7.1 0.00015 34.7 -0.3 33 6-42 109-141 (279)
29 PF14122 YokU: YokU-like prote 41.4 5.8 0.00013 29.8 -1.0 33 10-42 1-47 (87)
30 KOG1598 Transcription initiati 41.4 13 0.00029 35.7 1.2 30 9-41 1-30 (521)
31 PRK12286 rpmF 50S ribosomal pr 40.9 8.7 0.00019 26.3 -0.1 23 7-38 26-48 (57)
32 PRK14892 putative transcriptio 39.5 8.1 0.00018 29.3 -0.4 35 7-42 20-54 (99)
33 PF09526 DUF2387: Probable met 39.4 7.5 0.00016 27.8 -0.6 32 7-38 7-38 (71)
34 PF02701 zf-Dof: Dof domain, z 37.9 54 0.0012 23.4 3.5 48 5-53 2-52 (63)
35 smart00778 Prim_Zn_Ribbon Zinc 37.4 19 0.0004 22.9 1.0 29 8-37 3-32 (37)
36 PF01527 HTH_Tnp_1: Transposas 35.9 16 0.00034 24.5 0.6 24 142-165 1-24 (76)
37 PF06689 zf-C4_ClpX: ClpX C4-t 34.8 28 0.00062 22.0 1.6 33 9-42 2-36 (41)
38 PF04810 zf-Sec23_Sec24: Sec23 34.3 14 0.00031 23.2 0.1 32 7-38 1-32 (40)
39 PRK00085 recO DNA repair prote 33.9 19 0.00041 29.6 0.8 29 8-37 149-177 (247)
40 PF04161 Arv1: Arv1-like famil 33.1 18 0.00039 30.0 0.6 29 9-37 1-31 (208)
41 PF07282 OrfB_Zn_ribbon: Putat 32.1 21 0.00045 24.0 0.7 29 7-39 27-55 (69)
42 smart00834 CxxC_CXXC_SSSS Puta 30.9 15 0.00032 22.1 -0.2 29 9-38 6-34 (41)
43 PF12760 Zn_Tnp_IS1595: Transp 30.6 22 0.00047 22.7 0.5 27 8-37 18-44 (46)
44 PF09723 Zn-ribbon_8: Zinc rib 30.1 14 0.00031 23.3 -0.4 28 10-38 7-34 (42)
45 PRK00420 hypothetical protein; 30.1 20 0.00044 27.8 0.4 28 8-40 23-50 (112)
46 PLN03131 hypothetical protein; 28.8 30 0.00065 34.4 1.4 36 5-42 20-55 (705)
47 PF11304 DUF3106: Protein of u 28.5 54 0.0012 24.7 2.5 19 139-157 50-68 (107)
48 PF13240 zinc_ribbon_2: zinc-r 28.5 37 0.00079 19.2 1.2 20 11-38 2-21 (23)
49 KOG0021 Glutathione synthetase 28.4 30 0.00065 32.9 1.2 16 146-161 380-395 (468)
50 PRK08351 DNA-directed RNA poly 28.2 35 0.00076 23.9 1.3 16 9-24 16-32 (61)
51 TIGR02443 conserved hypothetic 27.6 16 0.00035 25.6 -0.5 31 8-38 9-39 (59)
52 smart00659 RPOLCX RNA polymera 27.5 20 0.00044 23.2 0.0 25 10-39 4-28 (44)
53 PLN03119 putative ADP-ribosyla 26.4 38 0.00082 33.5 1.6 46 5-52 20-65 (648)
54 PF09538 FYDLN_acid: Protein o 26.1 22 0.00047 27.3 -0.1 18 28-45 7-24 (108)
55 TIGR01031 rpmF_bact ribosomal 26.1 19 0.00041 24.4 -0.3 23 7-38 25-47 (55)
56 KOG3507 DNA-directed RNA polym 26.0 43 0.00093 23.8 1.4 27 9-40 21-47 (62)
57 PF09011 HMG_box_2: HMG-box do 25.7 72 0.0016 21.6 2.5 18 143-160 41-58 (73)
58 PHA00626 hypothetical protein 25.4 19 0.00041 25.4 -0.5 33 10-43 2-36 (59)
59 PF06945 DUF1289: Protein of u 25.4 58 0.0012 21.5 1.9 16 143-158 28-43 (51)
60 TIGR02605 CxxC_CxxC_SSSS putat 25.3 23 0.00051 22.6 -0.0 29 9-38 6-34 (52)
61 PRK06393 rpoE DNA-directed RNA 25.3 42 0.00091 23.8 1.3 16 8-23 17-33 (64)
62 KOG0706 Predicted GTPase-activ 24.8 31 0.00068 32.7 0.7 29 6-36 21-49 (454)
63 smart00661 RPOL9 RNA polymeras 24.6 38 0.00081 21.4 0.9 27 10-38 2-28 (52)
64 COG2331 Uncharacterized protei 23.8 28 0.00061 25.9 0.2 36 9-45 13-48 (82)
65 TIGR00244 transcriptional regu 22.8 34 0.00074 27.9 0.5 37 9-45 1-43 (147)
66 PF10080 DUF2318: Predicted me 22.7 14 0.0003 28.2 -1.7 28 10-42 37-64 (102)
67 PRK01110 rpmF 50S ribosomal pr 22.5 27 0.00058 24.1 -0.2 21 8-38 27-47 (60)
68 COG1405 SUA7 Transcription ini 22.3 32 0.00068 30.4 0.2 28 9-39 2-29 (285)
69 COG1734 DksA DnaK suppressor p 22.0 60 0.0013 25.4 1.7 38 6-44 78-115 (120)
70 cd07321 Extradiol_Dioxygenase_ 22.0 54 0.0012 23.4 1.3 11 147-157 34-44 (77)
71 COG1601 GCD7 Translation initi 22.0 29 0.00063 28.2 -0.1 31 7-38 104-134 (151)
72 PF02376 CUT: CUT domain; Int 21.4 98 0.0021 22.6 2.6 22 138-159 64-85 (87)
73 COG3952 Predicted membrane pro 21.1 27 0.00059 27.4 -0.4 17 21-39 76-92 (113)
74 COG5349 Uncharacterized protei 20.9 36 0.00078 27.2 0.2 32 9-43 22-53 (126)
75 cd07922 CarBa CarBa is the A s 20.8 72 0.0016 23.4 1.8 20 132-157 26-45 (81)
76 PRK05342 clpX ATP-dependent pr 20.5 87 0.0019 28.8 2.7 33 5-39 6-40 (412)
77 PF10083 DUF2321: Uncharacteri 20.4 41 0.00088 27.8 0.5 33 8-40 39-78 (158)
78 KOG1597 Transcription initiati 20.3 44 0.00095 30.3 0.7 31 10-41 2-32 (308)
79 PF02591 DUF164: Putative zinc 20.1 27 0.00058 23.0 -0.5 29 8-38 22-54 (56)
No 1
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.51 E-value=8.1e-15 Score=98.46 Aligned_cols=46 Identities=46% Similarity=0.988 Sum_probs=39.7
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHHHHHhhccccccCcc
Q 030971 7 NLKYCTDCKTTKTPLWRGGPAGPKSLCNACGIRFRKKKRVFEGLKK 52 (168)
Q Consensus 7 ~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~k~~~~~~~l~~ 52 (168)
....|++|+++.||+||+||.|+..|||+|||+|++.....+|+..
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~ 47 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSL 47 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCCCCcccc
Confidence 4689999999999999999999879999999988887665466554
No 2
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.51 E-value=9.1e-15 Score=99.15 Aligned_cols=43 Identities=53% Similarity=1.146 Sum_probs=36.6
Q ss_pred ccccCCCCCCCcccCCCCCCcccchHHHHHHHhhccccccCccc
Q 030971 10 YCTDCKTTKTPLWRGGPAGPKSLCNACGIRFRKKKRVFEGLKKR 53 (168)
Q Consensus 10 ~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~k~~~~~~~l~~~ 53 (168)
+|+||++++||+||+||+|..+|||||||||++.+ ..+|+...
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~-~~rp~~~~ 43 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG-VMRPLSKR 43 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC-CCCCcccC
Confidence 59999999999999999887999999999777765 56666553
No 3
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.44 E-value=2.4e-14 Score=89.66 Aligned_cols=34 Identities=53% Similarity=1.279 Sum_probs=26.7
Q ss_pred cccCCCCCCCcccCCCCCCcccchHHHHHHHhhc
Q 030971 11 CTDCKTTKTPLWRGGPAGPKSLCNACGIRFRKKK 44 (168)
Q Consensus 11 C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~k~~ 44 (168)
|++|++++||+||++|.|+.+|||+|||+|++.+
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 8999999999999999997779999999888765
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.71 E-value=7.2e-09 Score=81.38 Aligned_cols=44 Identities=61% Similarity=1.243 Sum_probs=37.6
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHHHHHhhccccccCcc
Q 030971 8 LKYCTDCKTTKTPLWRGGPAGPKSLCNACGIRFRKKKRVFEGLKK 52 (168)
Q Consensus 8 ~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~k~~~~~~~l~~ 52 (168)
...|.+|+++.||+||+++.|+.++||+||++|++.. +.+++.+
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~-~~r~~~~ 242 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGG-VRRPLPE 242 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcC-ccccccc
Confidence 5799999999999999999999999999999777665 5555544
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.18 E-value=4.5e-07 Score=84.62 Aligned_cols=44 Identities=43% Similarity=0.929 Sum_probs=39.9
Q ss_pred cccccCCCCCCCcccCCCC-----CCcccchHHHHHHHhhccccc-cCcccc
Q 030971 9 KYCTDCKTTKTPLWRGGPA-----GPKSLCNACGIRFRKKKRVFE-GLKKRS 54 (168)
Q Consensus 9 ~~C~~Cgtt~Tp~WRrGp~-----G~~~LCNACGL~y~k~~~~~~-~l~~~~ 54 (168)
.+|.||.|+.||+|||+.. | -+||||||| |.|.|+..+ |+..+.
T Consensus 159 ~vc~Nc~t~stPlwrR~~~~~s~~~-n~lcnaCgl-~~klhg~~r~P~t~ks 208 (498)
T COG5641 159 HVCSNCKTTSTPLWRRASSESSLPG-NNLCNACGL-YLKLHGSPRAPISLKS 208 (498)
T ss_pred chhccccccCCccccccccccccCC-ccccccccc-cccccCCcCCCccccc
Confidence 4899999999999999998 6 789999999 889999999 887665
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=93.61 E-value=0.061 Score=51.27 Aligned_cols=40 Identities=30% Similarity=0.612 Sum_probs=34.2
Q ss_pred CCCcccccCCCCCCCcc--cCCCCCCcccchHHHHHHHhhcc
Q 030971 6 SNLKYCTDCKTTKTPLW--RGGPAGPKSLCNACGIRFRKKKR 45 (168)
Q Consensus 6 ~~~~~C~~Cgtt~Tp~W--RrGp~G~~~LCNACGL~y~k~~~ 45 (168)
...+.|.+|+|++.-.| ..+|+-...||-.|=+||+|..+
T Consensus 384 ~~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKygG 425 (693)
T KOG3554|consen 384 QDGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYGG 425 (693)
T ss_pred CCCCcccccccccccceeccCCCCccchhhHHHHHHHHHhcC
Confidence 44789999999999999 55666667899999999999877
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=82.51 E-value=0.74 Score=43.71 Aligned_cols=44 Identities=32% Similarity=0.305 Sum_probs=34.2
Q ss_pred CcccccCCC-CCCCcccCCCCCCcccchHHHHHHHhhccccccCcc
Q 030971 8 LKYCTDCKT-TKTPLWRGGPAGPKSLCNACGIRFRKKKRVFEGLKK 52 (168)
Q Consensus 8 ~~~C~~Cgt-t~Tp~WRrGp~G~~~LCNACGL~y~k~~~~~~~l~~ 52 (168)
...|.+|.+ +.||.||+...---++||+||+ +.+..+..+++..
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~-~~~~~~~~~p~~p 341 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGS-ALKPPGSKRPLLP 341 (498)
T ss_pred hcCcccccccccCccccccccccccccccccc-ccCCcccccccCC
Confidence 456777877 7788888886554789999999 7777777777765
No 8
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=77.86 E-value=0.55 Score=29.27 Aligned_cols=30 Identities=27% Similarity=0.667 Sum_probs=15.3
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 9 KYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 9 ~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
+.|.+||..-+..--.|.+-...+|.+||-
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 469999988543322455666789999984
No 9
>PF15396 FAM60A: Protein Family FAM60A
Probab=77.67 E-value=0.79 Score=39.33 Aligned_cols=20 Identities=30% Similarity=0.674 Sum_probs=13.8
Q ss_pred cccchHHHHHHHhhcccccc
Q 030971 30 KSLCNACGIRFRKKKRVFEG 49 (168)
Q Consensus 30 ~~LCNACGL~y~k~~~~~~~ 49 (168)
+.+||||-|++++-++.+.+
T Consensus 49 GeICNACVLLVKRwKKLP~G 68 (213)
T PF15396_consen 49 GEICNACVLLVKRWKKLPPG 68 (213)
T ss_pred chhhHHHHHHHHHHhhCCCC
Confidence 35999999976666553333
No 10
>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=72.17 E-value=3.7 Score=31.01 Aligned_cols=38 Identities=29% Similarity=0.551 Sum_probs=26.0
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCcccchHHHHHHHhhc
Q 030971 5 DSNLKYCTDCKTTKTPLWRGGPAGPKSLCNACGIRFRKKK 44 (168)
Q Consensus 5 ~~~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~k~~ 44 (168)
..+...|++|+... |.|-.=.-| -.||-.|.-.++.+.
T Consensus 10 ~~~N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~lg 47 (116)
T PF01412_consen 10 KPGNKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRSLG 47 (116)
T ss_dssp STTCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHHHT
T ss_pred CcCcCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHHhc
Confidence 34568999999655 489999999 899999987666654
No 11
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=69.47 E-value=1.5 Score=33.71 Aligned_cols=29 Identities=28% Similarity=0.563 Sum_probs=21.5
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 9 KYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 9 ~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
..|..|+.++|-+=+.+..- -.-|+|||-
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 57999999999987763221 335999983
No 12
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=65.55 E-value=2.8 Score=37.71 Aligned_cols=30 Identities=40% Similarity=0.839 Sum_probs=27.4
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCcccchHH
Q 030971 5 DSNLKYCTDCKTTKTPLWRGGPAGPKSLCNAC 36 (168)
Q Consensus 5 ~~~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNAC 36 (168)
..+...|++|++.. |.|-.=.-| ..||-.|
T Consensus 17 ~~~Nk~CaDCga~~-P~W~S~nlG-vfiCi~C 46 (319)
T COG5347 17 DSSNKKCADCGAPN-PTWASVNLG-VFLCIDC 46 (319)
T ss_pred ccccCccccCCCCC-CceEecccC-eEEEeec
Confidence 45678999999999 999999999 8999999
No 13
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=65.25 E-value=1.8 Score=36.01 Aligned_cols=30 Identities=27% Similarity=0.562 Sum_probs=22.4
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 8 LKYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 8 ~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
-..|..|+.++|-+-+.+..- ..-|+|||-
T Consensus 98 yV~C~~C~~pdT~l~k~~~~~-~l~C~aCGa 127 (201)
T PRK12336 98 YVICSECGLPDTRLVKEDRVL-MLRCDACGA 127 (201)
T ss_pred eEECCCCCCCCcEEEEcCCeE-EEEcccCCC
Confidence 357999999999987653221 346999996
No 14
>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=59.54 E-value=7.9 Score=29.07 Aligned_cols=35 Identities=31% Similarity=0.579 Sum_probs=28.4
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHHHHHhh
Q 030971 7 NLKYCTDCKTTKTPLWRGGPAGPKSLCNACGIRFRKK 43 (168)
Q Consensus 7 ~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~k~ 43 (168)
+...|++|+. ..|.|-.-.-| ..||-.|.-..+.+
T Consensus 2 ~N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~l 36 (112)
T smart00105 2 GNKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRSL 36 (112)
T ss_pred CCCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHhc
Confidence 4578999998 55899998889 78999997755554
No 15
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=59.37 E-value=8.4 Score=26.81 Aligned_cols=31 Identities=29% Similarity=0.719 Sum_probs=24.1
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccc-hHHHHHHHhhcc
Q 030971 7 NLKYCTDCKTTKTPLWRGGPAGPKSLC-NACGIRFRKKKR 45 (168)
Q Consensus 7 ~~~~C~~Cgtt~Tp~WRrGp~G~~~LC-NACGL~y~k~~~ 45 (168)
..+-|.+||.+.-| . +.+| ..|+..|.+.++
T Consensus 2 ~HkHC~~CG~~Ip~-------~-~~fCS~~C~~~~~k~qk 33 (59)
T PF09889_consen 2 PHKHCPVCGKPIPP-------D-ESFCSPKCREEYRKRQK 33 (59)
T ss_pred CCCcCCcCCCcCCc-------c-hhhhCHHHHHHHHHHHH
Confidence 46789999977665 2 6799 699998887755
No 16
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=59.17 E-value=4.2 Score=40.07 Aligned_cols=37 Identities=27% Similarity=0.604 Sum_probs=28.9
Q ss_pred CCCcccccCCCCCCCcccCCCCC---CcccchHHHHHHHh
Q 030971 6 SNLKYCTDCKTTKTPLWRGGPAG---PKSLCNACGIRFRK 42 (168)
Q Consensus 6 ~~~~~C~~Cgtt~Tp~WRrGp~G---~~~LCNACGL~y~k 42 (168)
.++-.|..|.|.-||.|+.-+.+ .+.+|..|----.|
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 45678999999999999877665 35799999764333
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=57.88 E-value=3.5 Score=26.03 Aligned_cols=26 Identities=23% Similarity=0.813 Sum_probs=18.4
Q ss_pred ccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 10 YCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 10 ~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
.|.+|+.+. ..+- ...| ..+|..||+
T Consensus 2 ~Cp~Cg~~~-~~~D-~~~g-~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKE-IVFD-PERG-ELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSE-EEEE-TTTT-EEEETTT-B
T ss_pred CCcCCcCCc-eEEc-CCCC-eEECCCCCC
Confidence 699999977 3333 3356 779999997
No 18
>PF12773 DZR: Double zinc ribbon
Probab=53.43 E-value=8 Score=24.59 Aligned_cols=32 Identities=31% Similarity=0.781 Sum_probs=20.2
Q ss_pred CCCCCCCcccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 2 NQNDSNLKYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 2 ~~~~~~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
.+...+.+.|.+||+... .+.....+|..||-
T Consensus 6 ~~~~~~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 6 TPNPDDAKFCPHCGTPLP-----PPDQSKKICPNCGA 37 (50)
T ss_pred CcCCccccCChhhcCChh-----hccCCCCCCcCCcC
Confidence 345566788888888766 22222456777775
No 19
>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=53.17 E-value=7 Score=24.44 Aligned_cols=28 Identities=25% Similarity=0.617 Sum_probs=21.2
Q ss_pred CCCcccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 6 SNLKYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 6 ~~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
+....|..|+.. |-...+| ...|..||-
T Consensus 6 ~~~~~C~~C~~~----~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 6 GPNEPCPVCGSR----WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred cCCCcCCCCCCe----EeEccCC-EEEhhhCce
Confidence 334569999987 5556788 789999984
No 20
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=51.89 E-value=8 Score=35.95 Aligned_cols=32 Identities=34% Similarity=0.753 Sum_probs=26.9
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 5 DSNLKYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 5 ~~~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
..+.+.|.+|+... |.|-.-..| ..||..|.=
T Consensus 19 kPgNk~CaDCga~n-PtWASvn~G-IFLCl~CSG 50 (395)
T PLN03114 19 KSDNKICFDCNAKN-PTWASVTYG-IFLCIDCSA 50 (395)
T ss_pred CcCCCcCccCCCCC-CCceeeccc-eeehhhhhH
Confidence 34678999999865 899999999 889999944
No 21
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=50.12 E-value=11 Score=21.68 Aligned_cols=23 Identities=26% Similarity=0.876 Sum_probs=16.1
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 8 LKYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 8 ~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
.+.|.+|++...+ + ..+|-.||-
T Consensus 2 ~~~Cp~Cg~~~~~-------~-~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEIDP-------D-AKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCCc-------c-cccChhhCC
Confidence 3679999985433 3 458888885
No 22
>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=46.09 E-value=3.5 Score=27.84 Aligned_cols=22 Identities=41% Similarity=1.055 Sum_probs=15.9
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHH
Q 030971 7 NLKYCTDCKTTKTPLWRGGPAGPKSLCNACG 37 (168)
Q Consensus 7 ~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACG 37 (168)
....|.+||...- ++.+|..||
T Consensus 25 ~l~~c~~cg~~~~---------~H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKL---------PHRVCPSCG 46 (56)
T ss_dssp SEEESSSSSSEES---------TTSBCTTTB
T ss_pred ceeeeccCCCEec---------ccEeeCCCC
Confidence 4567888885433 367999999
No 23
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=45.98 E-value=8.9 Score=34.29 Aligned_cols=28 Identities=32% Similarity=0.782 Sum_probs=25.5
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHH
Q 030971 7 NLKYCTDCKTTKTPLWRGGPAGPKSLCNAC 36 (168)
Q Consensus 7 ~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNAC 36 (168)
+.+.|++|++. .|.|-.=.-| ..+|-.|
T Consensus 24 ~N~~CADC~a~-~P~WaSwnlG-vFiC~~C 51 (287)
T KOG0703|consen 24 DNKVCADCGAK-GPRWASWNLG-VFICLRC 51 (287)
T ss_pred ccCcccccCCC-CCCeEEeecC-eEEEeec
Confidence 47899999999 9999998889 8899999
No 24
>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=45.20 E-value=7.8 Score=25.06 Aligned_cols=25 Identities=48% Similarity=1.002 Sum_probs=18.6
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHH
Q 030971 8 LKYCTDCKTTKTPLWRGGPAGPKSLCNACG 37 (168)
Q Consensus 8 ~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACG 37 (168)
...|..| .+|+.| ..+| ..+|-.|+
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 3568888 589998 4466 67998885
No 25
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=44.78 E-value=9 Score=33.56 Aligned_cols=33 Identities=18% Similarity=0.633 Sum_probs=23.1
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCcccchHHHHHH
Q 030971 5 DSNLKYCTDCKTTKTPLWRGGPAGPKSLCNACGIRF 40 (168)
Q Consensus 5 ~~~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y 40 (168)
.+....|.+|+.+ ..+.. -..| ..+|..||+-+
T Consensus 8 ~~~~~~Cp~Cg~~-~iv~d-~~~G-e~vC~~CG~Vl 40 (310)
T PRK00423 8 EEEKLVCPECGSD-KLIYD-YERG-EIVCADCGLVI 40 (310)
T ss_pred cccCCcCcCCCCC-CeeEE-CCCC-eEeecccCCcc
Confidence 4556789999973 33333 3567 78999999943
No 26
>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=44.04 E-value=2.1 Score=25.53 Aligned_cols=28 Identities=29% Similarity=0.816 Sum_probs=16.3
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHHH
Q 030971 8 LKYCTDCKTTKTPLWRGGPAGPKSLCNACGIR 39 (168)
Q Consensus 8 ~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~ 39 (168)
.+.|..||....+. +.|....|.+||..
T Consensus 3 ~rfC~~CG~~t~~~----~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA----PGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-----SSSS-EEESSSS-E
T ss_pred CcccCcCCccccCC----CCcCEeECCCCcCE
Confidence 46899999987764 34556789999874
No 27
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=43.67 E-value=4.7 Score=28.78 Aligned_cols=33 Identities=18% Similarity=0.307 Sum_probs=24.5
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHHHH
Q 030971 8 LKYCTDCKTTKTPLWRGGPAGPKSLCNACGIRF 40 (168)
Q Consensus 8 ~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y 40 (168)
...|..|.+.+|-.|.+-..-+..-|-+||-.-
T Consensus 10 GA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~ 42 (66)
T COG3529 10 GAVCPACQAQDTLAMWRENNVEIVECVKCGHHM 42 (66)
T ss_pred cCCCcccchhhHHHHHHhcCCceEehhhcchHh
Confidence 457999999988775554444467899999743
No 28
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=43.22 E-value=7.1 Score=34.74 Aligned_cols=33 Identities=24% Similarity=0.593 Sum_probs=25.2
Q ss_pred CCCcccccCCCCCCCcccCCCCCCcccchHHHHHHHh
Q 030971 6 SNLKYCTDCKTTKTPLWRGGPAGPKSLCNACGIRFRK 42 (168)
Q Consensus 6 ~~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~k 42 (168)
...+.|..||+...+. ..|-..+|+.||..+..
T Consensus 109 ~~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~fP 141 (279)
T COG2816 109 RSHRFCGRCGTKTYPR----EGGWARVCPKCGHEHFP 141 (279)
T ss_pred hhCcCCCCCCCcCccc----cCceeeeCCCCCCccCC
Confidence 3468899999998874 34557799999986543
No 29
>PF14122 YokU: YokU-like protein
Probab=41.44 E-value=5.8 Score=29.84 Aligned_cols=33 Identities=27% Similarity=0.846 Sum_probs=21.0
Q ss_pred ccccCCCCC------CCccc--CC------CCCCcccchHHHHHHHh
Q 030971 10 YCTDCKTTK------TPLWR--GG------PAGPKSLCNACGIRFRK 42 (168)
Q Consensus 10 ~C~~Cgtt~------Tp~WR--rG------p~G~~~LCNACGL~y~k 42 (168)
.|..|+..+ |-.|- +| ++.|...|+.|||-|..
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~ 47 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQD 47 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEeh
Confidence 388898863 33352 22 23445689999997754
No 30
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=41.43 E-value=13 Score=35.71 Aligned_cols=30 Identities=23% Similarity=0.620 Sum_probs=21.0
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHHHHHH
Q 030971 9 KYCTDCKTTKTPLWRGGPAGPKSLCNACGIRFR 41 (168)
Q Consensus 9 ~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~ 41 (168)
+.|.||+.+.--. +-..| ...|++||...-
T Consensus 1 ~~C~~C~~s~fe~--d~a~g-~~~C~~CG~v~E 30 (521)
T KOG1598|consen 1 MVCKNCGGSNFER--DEATG-NLYCTACGTVLE 30 (521)
T ss_pred CcCCCCCCCCccc--ccccC-Cceeccccceee
Confidence 4699999886433 23345 679999998543
No 31
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=40.86 E-value=8.7 Score=26.33 Aligned_cols=23 Identities=35% Similarity=0.941 Sum_probs=17.7
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 7 NLKYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 7 ~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
..-.|.+||...-| +.+|..||.
T Consensus 26 ~l~~C~~CG~~~~~---------H~vC~~CG~ 48 (57)
T PRK12286 26 GLVECPNCGEPKLP---------HRVCPSCGY 48 (57)
T ss_pred cceECCCCCCccCC---------eEECCCCCc
Confidence 45578899887665 669999996
No 32
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=39.49 E-value=8.1 Score=29.33 Aligned_cols=35 Identities=14% Similarity=0.320 Sum_probs=21.6
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHHHHHh
Q 030971 7 NLKYCTDCKTTKTPLWRGGPAGPKSLCNACGIRFRK 42 (168)
Q Consensus 7 ~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~k 42 (168)
..-.|.+|+...-+. ..+...++..|..||.||..
T Consensus 20 t~f~CP~Cge~~v~v-~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGKVSISV-KIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCCeEeee-ecCCCcceEECCCCCCccCE
Confidence 345799999533222 11223447899999996544
No 33
>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=39.44 E-value=7.5 Score=27.81 Aligned_cols=32 Identities=19% Similarity=0.359 Sum_probs=25.2
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 7 NLKYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 7 ~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
..-.|..|+...|..|....+-...-|-+||-
T Consensus 7 AGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy 38 (71)
T PF09526_consen 7 AGAVCPKCQAMDTIMMWRENGVEYVECVECGY 38 (71)
T ss_pred cCccCCCCcCccEEEEEEeCCceEEEecCCCC
Confidence 34689999999998876655554667999997
No 34
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=37.92 E-value=54 Score=23.37 Aligned_cols=48 Identities=15% Similarity=0.389 Sum_probs=31.1
Q ss_pred CCCCcccccCCCCCCCcc--cC-CCCCCcccchHHHHHHHhhccccccCccc
Q 030971 5 DSNLKYCTDCKTTKTPLW--RG-GPAGPKSLCNACGIRFRKKKRVFEGLKKR 53 (168)
Q Consensus 5 ~~~~~~C~~Cgtt~Tp~W--Rr-Gp~G~~~LCNACGL~y~k~~~~~~~l~~~ 53 (168)
.++...|..|..+.|--= -. ...-|..+|-+|-.+|.... ..+-+...
T Consensus 2 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG-~lRnVPvg 52 (63)
T PF02701_consen 2 PEQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGG-TLRNVPVG 52 (63)
T ss_pred CccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcc-eecCCccC
Confidence 467889999999887542 22 22345679999999776544 34434333
No 35
>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=37.36 E-value=19 Score=22.85 Aligned_cols=29 Identities=21% Similarity=0.563 Sum_probs=21.4
Q ss_pred CcccccCCCCCCCcccCC-CCCCcccchHHH
Q 030971 8 LKYCTDCKTTKTPLWRGG-PAGPKSLCNACG 37 (168)
Q Consensus 8 ~~~C~~Cgtt~Tp~WRrG-p~G~~~LCNACG 37 (168)
...|..|+.+..=.|... ..| ..+|+.||
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G-~~~C~~Cg 32 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRG-TWFCSVCG 32 (37)
T ss_pred ccCCCCCCCccccccccCCCCc-CEEeCCCC
Confidence 457999999887667543 335 67999996
No 36
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=35.91 E-value=16 Score=24.47 Aligned_cols=24 Identities=17% Similarity=0.142 Sum_probs=14.4
Q ss_pred HHHHhhhhHHHHHHHHHHhhhccc
Q 030971 142 CQRKRKLKEEEQAAFSLMALSCGF 165 (168)
Q Consensus 142 ~~~~~~~~eee~aa~~lmals~g~ 165 (168)
|++|+..++|++..++-++|..|.
T Consensus 1 m~~r~~ys~e~K~~~v~~~~~~g~ 24 (76)
T PF01527_consen 1 MRKRRRYSPEFKLQAVREYLESGE 24 (76)
T ss_dssp --SS----HHHHHHHHHHHHHHHC
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCC
Confidence 566788999999999988876653
No 37
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=34.77 E-value=28 Score=22.01 Aligned_cols=33 Identities=24% Similarity=0.576 Sum_probs=19.9
Q ss_pred cccccCCCCCCCcc--cCCCCCCcccchHHHHHHHh
Q 030971 9 KYCTDCKTTKTPLW--RGGPAGPKSLCNACGIRFRK 42 (168)
Q Consensus 9 ~~C~~Cgtt~Tp~W--RrGp~G~~~LCNACGL~y~k 42 (168)
+.|+-||.+.+..= =.|++| ..+|+.|-.....
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~-~~IC~~Cv~~~~~ 36 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNG-AYICDECVEQAYE 36 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-S-EEEEHHHHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCC-cEECHHHHHHHHH
Confidence 57999999876442 256767 7899999875443
No 38
>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=34.30 E-value=14 Score=23.17 Aligned_cols=32 Identities=25% Similarity=0.602 Sum_probs=18.9
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 7 NLKYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 7 ~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
++.+|.+|++---|.-.=...|..-.||-|+.
T Consensus 1 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 1 GPVRCRRCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp -S-B-TTT--BS-TTSEEETTTTEEEETTT--
T ss_pred CccccCCCCCEECCcceEcCCCCEEECcCCCC
Confidence 35789999998888766566676679999986
No 39
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=33.95 E-value=19 Score=29.60 Aligned_cols=29 Identities=24% Similarity=0.646 Sum_probs=24.2
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHH
Q 030971 8 LKYCTDCKTTKTPLWRGGPAGPKSLCNACG 37 (168)
Q Consensus 8 ~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACG 37 (168)
...|..||+.....|-.-++| +.+|..|+
T Consensus 149 l~~C~~Cg~~~~~~~f~~~~g-g~~c~~c~ 177 (247)
T PRK00085 149 LDHCAVCGAPGDHRYFSPKEG-GAVCSECG 177 (247)
T ss_pred hhhHhcCCCCCCceEEecccC-Cccccccc
Confidence 458999999877777777788 88999997
No 40
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=33.07 E-value=18 Score=29.99 Aligned_cols=29 Identities=28% Similarity=0.694 Sum_probs=22.6
Q ss_pred cccccCCCCCCCcccCCCCCC--cccchHHH
Q 030971 9 KYCTDCKTTKTPLWRGGPAGP--KSLCNACG 37 (168)
Q Consensus 9 ~~C~~Cgtt~Tp~WRrGp~G~--~~LCNACG 37 (168)
.+|.+||.....+++.=..|. -+.|..||
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~ 31 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCG 31 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccC
Confidence 379999999988898765553 25799996
No 41
>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=32.08 E-value=21 Score=24.05 Aligned_cols=29 Identities=21% Similarity=0.557 Sum_probs=21.1
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHHH
Q 030971 7 NLKYCTDCKTTKTPLWRGGPAGPKSLCNACGIR 39 (168)
Q Consensus 7 ~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~ 39 (168)
....|..||..... ...+....|..||..
T Consensus 27 TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK----RRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCccccccc----ccccceEEcCCCCCE
Confidence 57789999987655 334446689999973
No 42
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS 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=30.88 E-value=15 Score=22.14 Aligned_cols=29 Identities=28% Similarity=0.554 Sum_probs=19.3
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 9 KYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 9 ~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
-.|.+|+..-+ .|..-.++....|-.||-
T Consensus 6 y~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFE-VLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEE-EEEecCCCCCCCCCCCCC
Confidence 36889998665 344433354567999987
No 43
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=30.59 E-value=22 Score=22.73 Aligned_cols=27 Identities=26% Similarity=0.500 Sum_probs=18.3
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHH
Q 030971 8 LKYCTDCKTTKTPLWRGGPAGPKSLCNACG 37 (168)
Q Consensus 8 ~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACG 37 (168)
...|.+|+.+ ...|-++ .+ ..-|++|+
T Consensus 18 g~~CP~Cg~~-~~~~~~~-~~-~~~C~~C~ 44 (46)
T PF12760_consen 18 GFVCPHCGST-KHYRLKT-RG-RYRCKACR 44 (46)
T ss_pred CCCCCCCCCe-eeEEeCC-CC-eEECCCCC
Confidence 3669999998 4444444 34 56888886
No 44
>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=30.14 E-value=14 Score=23.34 Aligned_cols=28 Identities=21% Similarity=0.430 Sum_probs=18.6
Q ss_pred ccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 10 YCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 10 ~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
.|.+||..-+-+..-.. .....|-.||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 68899977664443333 44568999885
No 45
>PRK00420 hypothetical protein; Validated
Probab=30.09 E-value=20 Score=27.79 Aligned_cols=28 Identities=29% Similarity=0.627 Sum_probs=20.3
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHHHH
Q 030971 8 LKYCTDCKTTKTPLWRGGPAGPKSLCNACGIRF 40 (168)
Q Consensus 8 ~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y 40 (168)
...|..|| +|+.+- .+| +.+|-.||-.+
T Consensus 23 ~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCG---LPLFEL-KDG-EVVCPVHGKVY 50 (112)
T ss_pred cCCCCCCC---Ccceec-CCC-ceECCCCCCee
Confidence 35788888 567663 456 77999999844
No 46
>PLN03131 hypothetical protein; Provisional
Probab=28.79 E-value=30 Score=34.42 Aligned_cols=36 Identities=17% Similarity=0.335 Sum_probs=27.7
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCcccchHHHHHHHh
Q 030971 5 DSNLKYCTDCKTTKTPLWRGGPAGPKSLCNACGIRFRK 42 (168)
Q Consensus 5 ~~~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~k 42 (168)
..+.+.|++|+... |.|-.-.-| ..||-.|.=..+.
T Consensus 20 ~PgNk~CADCga~~-P~WASiNlG-IFICi~CSGIHRs 55 (705)
T PLN03131 20 LPPNRRCINCNSLG-PQFVCTNFW-TFICMTCSGIHRE 55 (705)
T ss_pred CcCCCccccCCCCC-CCeeEeccc-eEEchhchhhhcc
Confidence 34568999999855 889998889 7899999432333
No 47
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=28.51 E-value=54 Score=24.71 Aligned_cols=19 Identities=21% Similarity=0.307 Sum_probs=13.6
Q ss_pred HHHHHHHhhhhHHHHHHHH
Q 030971 139 KQRCQRKRKLKEEEQAAFS 157 (168)
Q Consensus 139 ~~r~~~~~~~~eee~aa~~ 157 (168)
+.||.+|..|+.|||..+-
T Consensus 50 ~~rm~~W~~LspeqR~~~R 68 (107)
T PF11304_consen 50 RERMRRWAALSPEQRQQAR 68 (107)
T ss_pred HHHHHHHHhCCHHHHHHHH
Confidence 4567778888888877653
No 48
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=28.48 E-value=37 Score=19.17 Aligned_cols=20 Identities=25% Similarity=0.856 Sum_probs=12.1
Q ss_pred cccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 11 CTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 11 C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
|.+||..... + ..+|..||.
T Consensus 2 Cp~CG~~~~~-------~-~~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIED-------D-AKFCPNCGT 21 (23)
T ss_pred CcccCCCCCC-------c-CcchhhhCC
Confidence 6677766543 2 346777774
No 49
>KOG0021 consensus Glutathione synthetase [Secondary metabolites biosynthesis, transport and catabolism]
Probab=28.36 E-value=30 Score=32.90 Aligned_cols=16 Identities=50% Similarity=0.692 Sum_probs=13.7
Q ss_pred hhhhHHHHHHHHHHhh
Q 030971 146 RKLKEEEQAAFSLMAL 161 (168)
Q Consensus 146 ~~~~eee~aa~~lmal 161 (168)
+||.|||++|+.||-+
T Consensus 380 ~kl~~eer~AyILMe~ 395 (468)
T KOG0021|consen 380 KKLPEEERDAYILMEK 395 (468)
T ss_pred HhchhhhhhhhHHHHh
Confidence 4578889999999976
No 50
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=28.20 E-value=35 Score=23.94 Aligned_cols=16 Identities=19% Similarity=0.598 Sum_probs=12.3
Q ss_pred cccccCCCCC-CCcccC
Q 030971 9 KYCTDCKTTK-TPLWRG 24 (168)
Q Consensus 9 ~~C~~Cgtt~-Tp~WRr 24 (168)
..|.+|+++. |..|..
T Consensus 16 ~~CP~Cgs~~~T~~W~G 32 (61)
T PRK08351 16 DRCPVCGSRDLSDEWFD 32 (61)
T ss_pred CcCCCCcCCcccccccc
Confidence 3688888887 778874
No 51
>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=27.63 E-value=16 Score=25.65 Aligned_cols=31 Identities=19% Similarity=0.294 Sum_probs=23.4
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 8 LKYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 8 ~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
.-.|..|+...|-.|....+-...-|-.||-
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~ 39 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNIELVECVECGY 39 (59)
T ss_pred cccCCCCcCccEEEEEEeCCceEEEeccCCC
Confidence 4679999999988765444443567999996
No 52
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=27.45 E-value=20 Score=23.24 Aligned_cols=25 Identities=24% Similarity=0.635 Sum_probs=18.3
Q ss_pred ccccCCCCCCCcccCCCCCCcccchHHHHH
Q 030971 10 YCTDCKTTKTPLWRGGPAGPKSLCNACGIR 39 (168)
Q Consensus 10 ~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~ 39 (168)
.|.+||...+.. +.+ ..-|..||-+
T Consensus 4 ~C~~Cg~~~~~~----~~~-~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIK----SKD-VVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecC----CCC-ceECCCCCce
Confidence 699999987764 222 4579999964
No 53
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=26.43 E-value=38 Score=33.45 Aligned_cols=46 Identities=15% Similarity=0.262 Sum_probs=32.1
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCcccchHHHHHHHhhccccccCcc
Q 030971 5 DSNLKYCTDCKTTKTPLWRGGPAGPKSLCNACGIRFRKKKRVFEGLKK 52 (168)
Q Consensus 5 ~~~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~k~~~~~~~l~~ 52 (168)
..+.+.|++|+... |.|-.-.-| ..+|-.|.=..+.+..+-+.+.+
T Consensus 20 lPgNk~CADCgs~~-P~WASiNlG-IFICi~CSGIHRsLGhRVKSLSL 65 (648)
T PLN03119 20 LPPNRRCINCNSLG-PQYVCTTFW-TFVCMACSGIHREFTHRVKSVSM 65 (648)
T ss_pred CcCCCccccCCCCC-CCceeeccc-eEEeccchhhhccCCceeecccc
Confidence 34568999999866 899998899 78999995434444333333443
No 54
>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=26.13 E-value=22 Score=27.29 Aligned_cols=18 Identities=33% Similarity=0.874 Sum_probs=10.5
Q ss_pred CCcccchHHHHHHHhhcc
Q 030971 28 GPKSLCNACGIRFRKKKR 45 (168)
Q Consensus 28 G~~~LCNACGL~y~k~~~ 45 (168)
|.+-+|..||.+|+-+.+
T Consensus 7 GtKR~Cp~CG~kFYDLnk 24 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDLNK 24 (108)
T ss_pred CCcccCCCCcchhccCCC
Confidence 445566666666665555
No 55
>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=26.09 E-value=19 Score=24.40 Aligned_cols=23 Identities=35% Similarity=0.933 Sum_probs=15.8
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 7 NLKYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 7 ~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
..-.|.+||...-| +.+|-.||.
T Consensus 25 ~l~~C~~cG~~~~~---------H~vc~~cG~ 47 (55)
T TIGR01031 25 TLVVCPNCGEFKLP---------HRVCPSCGY 47 (55)
T ss_pred cceECCCCCCcccC---------eeECCccCe
Confidence 44568888875443 568888885
No 56
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=26.03 E-value=43 Score=23.76 Aligned_cols=27 Identities=33% Similarity=0.692 Sum_probs=19.8
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHHHHH
Q 030971 9 KYCTDCKTTKTPLWRGGPAGPKSLCNACGIRF 40 (168)
Q Consensus 9 ~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y 40 (168)
-+|.+|+...+-. .|...-|-.||-++
T Consensus 21 YiCgdC~~en~lk-----~~D~irCReCG~RI 47 (62)
T KOG3507|consen 21 YICGDCGQENTLK-----RGDVIRCRECGYRI 47 (62)
T ss_pred EEecccccccccc-----CCCcEehhhcchHH
Confidence 4799999988854 33345799999654
No 57
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins. It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....
Probab=25.67 E-value=72 Score=21.62 Aligned_cols=18 Identities=33% Similarity=0.475 Sum_probs=13.8
Q ss_pred HHHhhhhHHHHHHHHHHh
Q 030971 143 QRKRKLKEEEQAAFSLMA 160 (168)
Q Consensus 143 ~~~~~~~eee~aa~~lma 160 (168)
.+|+.|+++|++.+-=+|
T Consensus 41 ~~Wk~Ls~~EK~~Y~~~A 58 (73)
T PF09011_consen 41 ERWKSLSEEEKEPYEERA 58 (73)
T ss_dssp HHHHHS-HHHHHHHHHHH
T ss_pred HHHHhcCHHHHHHHHHHH
Confidence 579999999998876555
No 58
>PHA00626 hypothetical protein
Probab=25.43 E-value=19 Score=25.35 Aligned_cols=33 Identities=21% Similarity=0.430 Sum_probs=21.8
Q ss_pred ccccCCCCCCCc--ccCCCCCCcccchHHHHHHHhh
Q 030971 10 YCTDCKTTKTPL--WRGGPAGPKSLCNACGIRFRKK 43 (168)
Q Consensus 10 ~C~~Cgtt~Tp~--WRrGp~G~~~LCNACGL~y~k~ 43 (168)
.|.+|+...-.. -=+++.. .+.|..||-.|.+-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~sn-rYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSD-DYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCceeeeeceecccCc-ceEcCCCCCeechh
Confidence 589999854321 0124445 78999999877664
No 59
>PF06945 DUF1289: Protein of unknown function (DUF1289); InterPro: IPR010710 This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N terminus. The function of this family is unknown.
Probab=25.42 E-value=58 Score=21.50 Aligned_cols=16 Identities=13% Similarity=0.281 Sum_probs=13.5
Q ss_pred HHHhhhhHHHHHHHHH
Q 030971 143 QRKRKLKEEEQAAFSL 158 (168)
Q Consensus 143 ~~~~~~~eee~aa~~l 158 (168)
..|..|+++||.||+-
T Consensus 28 ~~W~~~s~~er~~i~~ 43 (51)
T PF06945_consen 28 RDWKSMSDDERRAILA 43 (51)
T ss_pred HHHhhCCHHHHHHHHH
Confidence 3699999999999874
No 60
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=25.33 E-value=23 Score=22.62 Aligned_cols=29 Identities=24% Similarity=0.507 Sum_probs=20.1
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 9 KYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 9 ~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
-.|.+|+..-+ .|+.-.+.....|-.||-
T Consensus 6 y~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFE-VLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeE-EEEecCCCCCCCCCCCCC
Confidence 36999998666 576543333567999996
No 61
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=25.31 E-value=42 Score=23.85 Aligned_cols=16 Identities=31% Similarity=0.391 Sum_probs=11.4
Q ss_pred CcccccCCCCC-CCccc
Q 030971 8 LKYCTDCKTTK-TPLWR 23 (168)
Q Consensus 8 ~~~C~~Cgtt~-Tp~WR 23 (168)
...|.+||++. |+.|.
T Consensus 17 ~~~Cp~Cgs~~~S~~w~ 33 (64)
T PRK06393 17 EKTCPVHGDEKTTTEWF 33 (64)
T ss_pred CCcCCCCCCCcCCcCcc
Confidence 34788888876 66675
No 62
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=24.78 E-value=31 Score=32.73 Aligned_cols=29 Identities=38% Similarity=0.785 Sum_probs=25.4
Q ss_pred CCCcccccCCCCCCCcccCCCCCCcccchHH
Q 030971 6 SNLKYCTDCKTTKTPLWRGGPAGPKSLCNAC 36 (168)
Q Consensus 6 ~~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNAC 36 (168)
.+.+.|.+|+.. .|.|-.=+.| -.||-.|
T Consensus 21 ~~NKvCFDCgAk-nPtWaSVTYG-IFLCiDC 49 (454)
T KOG0706|consen 21 SENKVCFDCGAK-NPTWASVTYG-IFLCIDC 49 (454)
T ss_pred CCCceecccCCC-CCCceeecce-EEEEEec
Confidence 467899999975 4679999999 8999999
No 63
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=24.63 E-value=38 Score=21.40 Aligned_cols=27 Identities=26% Similarity=0.790 Sum_probs=17.6
Q ss_pred ccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 10 YCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 10 ~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
.|.+||..-.+. .+......+|..||-
T Consensus 2 FCp~Cg~~l~~~--~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNMLIPK--EGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCccccc--cCCCCCEEECCcCCC
Confidence 699999865443 111223678999995
No 64
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.78 E-value=28 Score=25.88 Aligned_cols=36 Identities=25% Similarity=0.573 Sum_probs=23.7
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHHHHHHhhcc
Q 030971 9 KYCTDCKTTKTPLWRGGPAGPKSLCNACGIRFRKKKR 45 (168)
Q Consensus 9 ~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~k~~~ 45 (168)
-.|.+|+-..+-+ +.-.+.|-+.|.+||-+++|...
T Consensus 13 Y~c~~cg~~~dvv-q~~~ddplt~ce~c~a~~kk~l~ 48 (82)
T COG2331 13 YECTECGNRFDVV-QAMTDDPLTTCEECGARLKKLLN 48 (82)
T ss_pred EeecccchHHHHH-HhcccCccccChhhChHHHHhhc
Confidence 3688998765533 22223344589999998888755
No 65
>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=22.76 E-value=34 Score=27.89 Aligned_cols=37 Identities=27% Similarity=0.468 Sum_probs=26.9
Q ss_pred cccccCCCCCCCcc--cCCCCCC----cccchHHHHHHHhhcc
Q 030971 9 KYCTDCKTTKTPLW--RGGPAGP----KSLCNACGIRFRKKKR 45 (168)
Q Consensus 9 ~~C~~Cgtt~Tp~W--RrGp~G~----~~LCNACGL~y~k~~~ 45 (168)
+.|..|+...|-.- |-..+|. .-.|.+||-+|.-.-.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyEr 43 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFER 43 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeee
Confidence 46999999998875 4455563 2479999988766544
No 66
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=22.70 E-value=14 Score=28.18 Aligned_cols=28 Identities=29% Similarity=0.713 Sum_probs=17.4
Q ss_pred ccccCCCCCCCcccCCCCCCcccchHHHHHHHh
Q 030971 10 YCTDCKTTKTPLWRGGPAGPKSLCNACGIRFRK 42 (168)
Q Consensus 10 ~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~k 42 (168)
.|.-|+-..=- ..|...+|++||.+|..
T Consensus 37 aCeiC~~~GY~-----q~g~~lvC~~C~~~~~~ 64 (102)
T PF10080_consen 37 ACEICGPKGYY-----QEGDQLVCKNCGVRFNL 64 (102)
T ss_pred eccccCCCceE-----EECCEEEEecCCCEEeh
Confidence 57777332211 24557899999987654
No 67
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=22.46 E-value=27 Score=24.13 Aligned_cols=21 Identities=14% Similarity=0.124 Sum_probs=14.2
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 8 LKYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 8 ~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
...|.+||...-| +.+|. ||.
T Consensus 27 ~~~c~~cg~~~~p---------H~vc~-cG~ 47 (60)
T PRK01110 27 LSVDKTTGEYHLP---------HHVSP-KGY 47 (60)
T ss_pred eeEcCCCCceecc---------ceecC-Ccc
Confidence 4567777776554 45788 886
No 68
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=22.30 E-value=32 Score=30.44 Aligned_cols=28 Identities=25% Similarity=0.661 Sum_probs=19.5
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHHHH
Q 030971 9 KYCTDCKTTKTPLWRGGPAGPKSLCNACGIR 39 (168)
Q Consensus 9 ~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~ 39 (168)
..|.+|+.+. -.| .-..| ..+|-.||+-
T Consensus 2 ~~CpeCg~~~-~~~-d~~~g-e~VC~~CG~V 29 (285)
T COG1405 2 MSCPECGSTN-IIT-DYERG-EIVCADCGLV 29 (285)
T ss_pred CCCCCCCCcc-cee-eccCC-eEEeccCCEE
Confidence 4799999982 222 22357 7899999984
No 69
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=22.02 E-value=60 Score=25.38 Aligned_cols=38 Identities=16% Similarity=0.382 Sum_probs=29.3
Q ss_pred CCCcccccCCCCCCCcccCCCCCCcccchHHHHHHHhhc
Q 030971 6 SNLKYCTDCKTTKTPLWRGGPAGPKSLCNACGIRFRKKK 44 (168)
Q Consensus 6 ~~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~k~~ 44 (168)
+....|..||-...+..+..-.+ ..+|..|--.+-+..
T Consensus 78 gtYG~Ce~cG~~Ip~~RL~A~P~-A~~Ci~cQ~~~E~~~ 115 (120)
T COG1734 78 GTYGICEECGEPIPEARLEARPT-ARLCIECQERAERRE 115 (120)
T ss_pred CCccchhccCCcCCHHHHhhCcc-hHHHHHHHHHHHHHH
Confidence 45568999999988887777666 679999987665544
No 70
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=21.99 E-value=54 Score=23.38 Aligned_cols=11 Identities=45% Similarity=0.483 Sum_probs=9.7
Q ss_pred hhhHHHHHHHH
Q 030971 147 KLKEEEQAAFS 157 (168)
Q Consensus 147 ~~~eee~aa~~ 157 (168)
-|+|||++||+
T Consensus 34 ~Lt~eE~~al~ 44 (77)
T cd07321 34 GLTPEEKAALL 44 (77)
T ss_pred CCCHHHHHHHH
Confidence 59999999985
No 71
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=21.95 E-value=29 Score=28.23 Aligned_cols=31 Identities=26% Similarity=0.509 Sum_probs=23.6
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHH
Q 030971 7 NLKYCTDCKTTKTPLWRGGPAGPKSLCNACGI 38 (168)
Q Consensus 7 ~~~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL 38 (168)
....|..|+...|++-+.+-.- ...|-|||-
T Consensus 104 ~yv~C~~c~s~dt~l~~~~R~~-~l~c~acGa 134 (151)
T COG1601 104 EYVKCKECGSPDTELIKEERLL-FLKCEACGA 134 (151)
T ss_pred heeEeccCCCCchhhhhhhhhH-hhHHHHhCC
Confidence 3468999999999997763222 457999997
No 72
>PF02376 CUT: CUT domain; InterPro: IPR003350 A class, also called ONECUT, of homeodomain proteins. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain (IPR001356 from INTERPRO), often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the cut domain, and two modes of transcriptional stimulation, which hinge on the homeodomain [].; GO: 0003677 DNA binding; PDB: 1WH6_A 2D5V_A 2CSF_A 1X2L_A 2O49_A 2O4A_A 1YSE_A 1S7E_A 1WIZ_A 1WH8_A.
Probab=21.43 E-value=98 Score=22.63 Aligned_cols=22 Identities=27% Similarity=0.128 Sum_probs=19.5
Q ss_pred HHHHHHHHhhhhHHHHHHHHHH
Q 030971 138 KKQRCQRKRKLKEEEQAAFSLM 159 (168)
Q Consensus 138 ~~~r~~~~~~~~eee~aa~~lm 159 (168)
.=.||.-|=++.|+|+.+++-|
T Consensus 64 ~y~RM~nWL~~~e~~r~~i~~~ 85 (87)
T PF02376_consen 64 PYIRMYNWLSLPEEERMEILKM 85 (87)
T ss_dssp HHHHHHHHHCSTHHHHHHHHHH
T ss_pred HHHHHHHHhcCCHHHHHHHHhc
Confidence 3568999999999999999987
No 73
>COG3952 Predicted membrane protein [Function unknown]
Probab=21.10 E-value=27 Score=27.36 Aligned_cols=17 Identities=35% Similarity=0.575 Sum_probs=12.8
Q ss_pred cccCCCCCCcccchHHHHH
Q 030971 21 LWRGGPAGPKSLCNACGIR 39 (168)
Q Consensus 21 ~WRrGp~G~~~LCNACGL~ 39 (168)
+||.+|-+ .+|++||+.
T Consensus 76 i~~~DpV~--Vl~~~~glF 92 (113)
T COG3952 76 IRRQDPVF--VLGQACGLF 92 (113)
T ss_pred HHhcchHH--HHHHhhhHH
Confidence 36666666 499999994
No 74
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.85 E-value=36 Score=27.21 Aligned_cols=32 Identities=28% Similarity=0.673 Sum_probs=17.8
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHHHHHHhh
Q 030971 9 KYCTDCKTTKTPLWRGGPAGPKSLCNACGIRFRKK 43 (168)
Q Consensus 9 ~~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~k~ 43 (168)
-.|-+||--. +.|. =--..+-|.+||+-|...
T Consensus 22 grCP~CGeGr--LF~g-FLK~~p~C~aCG~dyg~~ 53 (126)
T COG5349 22 GRCPRCGEGR--LFRG-FLKVVPACEACGLDYGFA 53 (126)
T ss_pred CCCCCCCCch--hhhh-hcccCchhhhccccccCC
Confidence 4567776432 2222 122246799999877544
No 75
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=20.83 E-value=72 Score=23.40 Aligned_cols=20 Identities=35% Similarity=0.366 Sum_probs=13.8
Q ss_pred chhHHHHHHHHHHHhhhhHHHHHHHH
Q 030971 132 LPSVVAKKQRCQRKRKLKEEEQAAFS 157 (168)
Q Consensus 132 ~~~~~~~~~r~~~~~~~~eee~aa~~ 157 (168)
.|.-|-+++ -|+|||++|+.
T Consensus 26 DPea~~~~~------gLt~eE~~aL~ 45 (81)
T cd07922 26 DPSAVFEEY------GLTPAERAALR 45 (81)
T ss_pred CHHHHHHHc------CCCHHHHHHHH
Confidence 455554433 49999999975
No 76
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=20.45 E-value=87 Score=28.81 Aligned_cols=33 Identities=27% Similarity=0.671 Sum_probs=22.7
Q ss_pred CCCCcccccCCCCCCCcc--cCCCCCCcccchHHHHH
Q 030971 5 DSNLKYCTDCKTTKTPLW--RGGPAGPKSLCNACGIR 39 (168)
Q Consensus 5 ~~~~~~C~~Cgtt~Tp~W--RrGp~G~~~LCNACGL~ 39 (168)
......|+.||.+....= -.|| + .++|+.|--.
T Consensus 6 ~~~~~~CSFCGr~~~ev~~li~g~-~-~~IC~~Ci~~ 40 (412)
T PRK05342 6 SKKLLYCSFCGKSQHEVRKLIAGP-G-VYICDECIEL 40 (412)
T ss_pred CCCccccCCCCCChhhccccccCC-C-CcccchHHHH
Confidence 455669999999866542 3455 3 4699999543
No 77
>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=20.42 E-value=41 Score=27.83 Aligned_cols=33 Identities=24% Similarity=0.601 Sum_probs=21.9
Q ss_pred CcccccCCCCCCCcccC-------CCCCCcccchHHHHHH
Q 030971 8 LKYCTDCKTTKTPLWRG-------GPAGPKSLCNACGIRF 40 (168)
Q Consensus 8 ~~~C~~Cgtt~Tp~WRr-------Gp~G~~~LCNACGL~y 40 (168)
...|.+|++..--.|-- ++.-.-..|+.||..|
T Consensus 39 I~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 39 ITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCC
Confidence 45789998887666643 2233335899999864
No 78
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=20.26 E-value=44 Score=30.31 Aligned_cols=31 Identities=32% Similarity=0.800 Sum_probs=23.1
Q ss_pred ccccCCCCCCCcccCCCCCCcccchHHHHHHH
Q 030971 10 YCTDCKTTKTPLWRGGPAGPKSLCNACGIRFR 41 (168)
Q Consensus 10 ~C~~Cgtt~Tp~WRrGp~G~~~LCNACGL~y~ 41 (168)
.|..|......+--+--.| .++|-.|||-+.
T Consensus 2 ~c~~C~~~~~~~V~d~~~g-dtvC~~CGlVl~ 32 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAG-DTVCSECGLVLE 32 (308)
T ss_pred CCCCCCCCCCCeeeeccCC-ceecccCCeeec
Confidence 5889988766555555667 789999999543
No 79
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=20.09 E-value=27 Score=23.03 Aligned_cols=29 Identities=28% Similarity=0.585 Sum_probs=21.6
Q ss_pred CcccccCCCCCCCcc----cCCCCCCcccchHHHH
Q 030971 8 LKYCTDCKTTKTPLW----RGGPAGPKSLCNACGI 38 (168)
Q Consensus 8 ~~~C~~Cgtt~Tp~W----RrGp~G~~~LCNACGL 38 (168)
...|..|+..-+|.+ +++ +. -..|..||-
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~-~~-i~~Cp~CgR 54 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKG-DE-IVFCPNCGR 54 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcC-CC-eEECcCCCc
Confidence 458999999998884 455 33 468999985
Done!