Query 023588
Match_columns 280
No_of_seqs 139 out of 700
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 05:10:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023588.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023588hhsearch_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 9.8E-15 2.1E-19 106.2 4.1 44 212-258 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.5 1.1E-14 2.4E-19 104.8 3.2 40 209-248 2-41 (52)
3 PF00320 GATA: GATA zinc finge 99.5 1E-14 2.2E-19 98.1 0.2 35 213-247 1-35 (36)
4 KOG1601 GATA-4/5/6 transcripti 99.2 1.5E-11 3.2E-16 102.5 4.6 70 210-279 199-302 (340)
5 COG5641 GAT1 GATA Zn-finger-co 97.8 9.2E-06 2E-10 81.6 1.7 54 210-265 158-215 (498)
6 KOG3554 Histone deacetylase co 94.1 0.094 2E-06 53.8 5.8 37 208-244 384-422 (693)
7 COG5641 GAT1 GATA Zn-finger-co 75.9 1.5 3.2E-05 45.0 1.6 39 210-248 297-336 (498)
8 PF14803 Nudix_N_2: Nudix N-te 56.3 2.1 4.6E-05 29.0 -1.2 30 211-240 1-30 (34)
9 PRK14892 putative transcriptio 49.2 6.1 0.00013 32.5 0.2 35 209-244 20-54 (99)
10 PF01412 ArfGap: Putative GTPa 49.2 12 0.00027 30.4 2.0 35 208-244 11-45 (116)
11 COG5347 GTPase-activating prot 49.0 6.3 0.00014 38.3 0.3 35 208-244 18-52 (319)
12 PRK03988 translation initiatio 47.5 4.4 9.5E-05 34.9 -0.9 30 211-241 103-132 (138)
13 KOG3740 Uncharacterized conser 46.2 12 0.00027 39.8 1.9 36 207-242 459-497 (706)
14 TIGR00311 aIF-2beta translatio 45.7 5.1 0.00011 34.3 -0.8 31 211-242 98-128 (133)
15 PF15468 DUF4636: Domain of un 44.9 9 0.0002 36.1 0.6 76 138-224 131-209 (243)
16 PF02701 zf-Dof: Dof domain, z 43.4 37 0.0008 26.4 3.6 46 209-254 4-52 (63)
17 PF01783 Ribosomal_L32p: Ribos 43.1 5.7 0.00012 29.1 -0.8 25 209-243 25-49 (56)
18 smart00653 eIF2B_5 domain pres 42.3 6.1 0.00013 32.8 -0.8 29 211-240 81-109 (110)
19 PLN03114 ADP-ribosylation fact 40.6 16 0.00034 36.8 1.6 45 209-255 21-66 (395)
20 PRK12336 translation initiatio 40.0 6.7 0.00015 35.3 -1.0 33 211-244 99-131 (201)
21 PRK13130 H/ACA RNA-protein com 38.6 31 0.00066 25.9 2.5 49 209-276 4-52 (56)
22 TIGR01385 TFSII transcription 36.8 11 0.00024 36.1 -0.1 37 207-243 255-297 (299)
23 PF13248 zf-ribbon_3: zinc-rib 35.9 21 0.00045 22.3 1.1 23 211-241 3-25 (26)
24 PF08271 TF_Zn_Ribbon: TFIIB z 34.7 8 0.00017 26.4 -1.0 30 212-244 2-31 (43)
25 PF04810 zf-Sec23_Sec24: Sec23 33.7 11 0.00025 25.7 -0.4 31 210-240 2-32 (40)
26 smart00105 ArfGap Putative GTP 33.4 31 0.00067 28.0 2.0 34 209-244 2-35 (112)
27 PF15396 FAM60A: Protein Famil 33.0 22 0.00048 33.2 1.2 18 232-249 49-66 (213)
28 PF01096 TFIIS_C: Transcriptio 32.8 4.1 9E-05 27.8 -2.7 32 212-243 2-39 (39)
29 COG2816 NPY1 NTP pyrophosphohy 32.7 15 0.00033 35.3 0.1 30 209-242 110-139 (279)
30 PF07282 OrfB_Zn_ribbon: Putat 31.7 20 0.00043 26.1 0.6 31 209-243 27-57 (69)
31 PF11781 RRN7: RNA polymerase 30.8 23 0.00049 24.1 0.7 26 210-240 8-33 (36)
32 PF10083 DUF2321: Uncharacteri 30.6 32 0.00069 30.9 1.7 33 210-242 39-78 (158)
33 COG3952 Predicted membrane pro 29.0 19 0.00041 30.7 0.1 18 224-243 77-94 (113)
34 PF01873 eIF-5_eIF-2B: Domain 29.0 11 0.00024 31.9 -1.3 29 211-240 94-122 (125)
35 PF14122 YokU: YokU-like prote 27.7 13 0.00028 30.4 -1.1 33 212-244 1-47 (87)
36 KOG1598 Transcription initiati 27.3 30 0.00064 36.1 1.1 49 211-262 1-51 (521)
37 cd07160 NR_DBD_LXR DNA-binding 27.2 46 0.00099 27.2 2.0 31 209-244 17-47 (101)
38 PRK12286 rpmF 50S ribosomal pr 26.8 18 0.00038 27.0 -0.4 25 208-241 25-49 (57)
39 PF12760 Zn_Tnp_IS1595: Transp 26.7 21 0.00046 24.8 -0.0 27 211-240 19-45 (46)
40 COG3529 Predicted nucleic-acid 26.0 12 0.00027 29.0 -1.4 35 210-244 10-44 (66)
41 PF12773 DZR: Double zinc ribb 25.6 30 0.00064 23.8 0.5 30 209-243 11-40 (50)
42 TIGR00244 transcriptional regu 25.5 28 0.0006 30.8 0.5 34 212-245 2-41 (147)
43 KOG3413 Mitochondrial matrix p 24.7 43 0.00092 30.0 1.5 28 11-39 51-78 (156)
44 smart00778 Prim_Zn_Ribbon Zinc 24.2 42 0.00091 23.2 1.0 30 211-240 4-33 (37)
45 PHA02998 RNA polymerase subuni 23.8 22 0.00048 32.7 -0.5 36 209-244 142-183 (195)
46 KOG0909 Peptide:N-glycanase [P 23.4 28 0.0006 36.0 0.1 32 210-241 161-203 (500)
47 PRK00420 hypothetical protein; 22.3 27 0.00059 29.4 -0.2 30 210-244 23-52 (112)
48 PLN03131 hypothetical protein; 22.2 42 0.00091 36.1 1.1 34 208-243 21-54 (705)
49 PRK00085 recO DNA repair prote 21.9 33 0.00072 30.4 0.3 29 210-239 149-177 (247)
50 TIGR03573 WbuX N-acetyl sugar 21.4 59 0.0013 31.1 1.9 30 211-243 2-32 (343)
51 smart00440 ZnF_C2C2 C2C2 Zinc 21.3 18 0.0004 24.8 -1.2 32 212-243 2-39 (40)
52 PLN03119 putative ADP-ribosyla 20.9 42 0.0009 35.8 0.8 34 208-243 21-54 (648)
53 PRK00423 tfb transcription ini 20.8 37 0.00081 32.1 0.4 11 232-242 30-40 (310)
54 PRK00241 nudC NADH pyrophospha 20.4 28 0.00061 32.2 -0.5 29 209-241 98-126 (256)
55 cd07169 NR_DBD_GCNF_like DNA-b 20.3 63 0.0014 25.7 1.5 31 209-244 5-35 (90)
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=9.8e-15 Score=106.21 Aligned_cols=44 Identities=41% Similarity=0.939 Sum_probs=38.1
Q ss_pred ccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhhCCCCCCCCCCCCCC
Q 023588 212 KCMHCEVAETPQWREGPMGPKTLCNACGVRYRSGRLVPEYRPAASPT 258 (280)
Q Consensus 212 ~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk~r~~p~yrpa~spt 258 (280)
.|+||+++.||+||+||+|..+|||||||+|++++ ..+|...+.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~---~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG---VMRPLSKRK 44 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC---CCCCcccCc
Confidence 59999999999999999999999999999999976 455655443
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.50 E-value=1.1e-14 Score=104.85 Aligned_cols=40 Identities=50% Similarity=1.068 Sum_probs=36.3
Q ss_pred CCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhhCCCC
Q 023588 209 TPRKCMHCEVAETPQWREGPMGPKTLCNACGVRYRSGRLV 248 (280)
Q Consensus 209 ~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk~r~~ 248 (280)
..+.|.||+++.||+||+||.|..+|||||||+|++.+.+
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 3578999999999999999999889999999999996554
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=99.45 E-value=1e-14 Score=98.07 Aligned_cols=35 Identities=54% Similarity=1.184 Sum_probs=28.3
Q ss_pred cCcCCCCCCCCcCCCCCCChhHhHHhhhHHhhCCC
Q 023588 213 CMHCEVAETPQWREGPMGPKTLCNACGVRYRSGRL 247 (280)
Q Consensus 213 C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk~r~ 247 (280)
|.||++++||+||+||.|..+||||||++|++++.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 89999999999999999988999999999999764
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=99.20 E-value=1.5e-11 Score=102.53 Aligned_cols=70 Identities=57% Similarity=1.131 Sum_probs=61.3
Q ss_pred CCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhhC---CCCCCCCCCCCCC--------------cccccccc------
Q 023588 210 PRKCMHCEVAETPQWREGPMGPKTLCNACGVRYRSG---RLVPEYRPAASPT--------------FVPSLHSN------ 266 (280)
Q Consensus 210 ~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk~---r~~p~yrpa~spt--------------f~p~~~s~------ 266 (280)
...|.+|+++.||+||+++.|.+.+|||||++|+++ +.++.++.+..++ +....|.+
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPRNVSPKGSGAVKGRTFTKSLHSNSAQLLL 278 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCccccccccCccccccccCCCccccccCCCCCcccccchhhhhh
Confidence 579999999999999999999999999999999998 7788888888777 56666666
Q ss_pred -----------chHHHHHhhhcCC
Q 023588 267 -----------SHKRIMEMRNKGR 279 (280)
Q Consensus 267 -----------~h~kv~~~r~k~~ 279 (280)
.|.++.++++..+
T Consensus 279 ~~~~~~~~~~~~~~~~~~~~r~~~ 302 (340)
T KOG1601|consen 279 APSKSEPPLLSSHQRVAEVRRYRE 302 (340)
T ss_pred hhcccCccccccchHHHHHhhccC
Confidence 8899999887654
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=97.77 E-value=9.2e-06 Score=81.58 Aligned_cols=54 Identities=28% Similarity=0.557 Sum_probs=41.4
Q ss_pred CCccCcCCCCCCCCcCCCCCC----ChhHhHHhhhHHhhCCCCCCCCCCCCCCccccccc
Q 023588 210 PRKCMHCEVAETPQWREGPMG----PKTLCNACGVRYRSGRLVPEYRPAASPTFVPSLHS 265 (280)
Q Consensus 210 ~~~C~~Cgvt~TP~WR~GP~G----~~tLCNACGL~~kk~r~~p~yrpa~sptf~p~~~s 265 (280)
..+|.+|.++.||+|||+..+ .-.|||||||+|+-.+..-+ |...++.+.+-|.
T Consensus 158 ~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~--P~t~ks~~~ks~~ 215 (498)
T COG5641 158 PHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRA--PISLKSDSIKSRS 215 (498)
T ss_pred cchhccccccCCccccccccccccCCccccccccccccccCCcCC--Ccccccccccccc
Confidence 348999999999999999994 37999999999998766543 5555555444333
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=94.14 E-value=0.094 Score=53.78 Aligned_cols=37 Identities=24% Similarity=0.602 Sum_probs=31.9
Q ss_pred CCCCccCcCCCCCCCCc--CCCCCCChhHhHHhhhHHhh
Q 023588 208 DTPRKCMHCEVAETPQW--REGPMGPKTLCNACGVRYRS 244 (280)
Q Consensus 208 ~~~~~C~~Cgvt~TP~W--R~GP~G~~tLCNACGL~~kk 244 (280)
..++.|.+|+++..-+| +-+|+-...||-.|.++|+|
T Consensus 384 ~~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKK 422 (693)
T KOG3554|consen 384 QDGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKK 422 (693)
T ss_pred CCCCcccccccccccceeccCCCCccchhhHHHHHHHHH
Confidence 34679999999999999 55666667899999999999
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=75.86 E-value=1.5 Score=44.97 Aligned_cols=39 Identities=23% Similarity=0.335 Sum_probs=32.3
Q ss_pred CCccCcCCC-CCCCCcCCCCCCChhHhHHhhhHHhhCCCC
Q 023588 210 PRKCMHCEV-AETPQWREGPMGPKTLCNACGVRYRSGRLV 248 (280)
Q Consensus 210 ~~~C~~Cgv-t~TP~WR~GP~G~~tLCNACGL~~kk~r~~ 248 (280)
...|.+|++ +.||.||+...-.-++|||||++.+..+..
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~ 336 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPGSK 336 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCCcccc
Confidence 457888876 789999999888789999999999885553
No 8
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=56.29 E-value=2.1 Score=28.99 Aligned_cols=30 Identities=27% Similarity=0.576 Sum_probs=15.3
Q ss_pred CccCcCCCCCCCCcCCCCCCChhHhHHhhh
Q 023588 211 RKCMHCEVAETPQWREGPMGPKTLCNACGV 240 (280)
Q Consensus 211 ~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL 240 (280)
+.|.+||..-+-.=-.|.+-.+.+|.+||-
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 368999987433333566666789999984
No 9
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=49.21 E-value=6.1 Score=32.50 Aligned_cols=35 Identities=14% Similarity=0.211 Sum_probs=22.4
Q ss_pred CCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhh
Q 023588 209 TPRKCMHCEVAETPQWREGPMGPKTLCNACGVRYRS 244 (280)
Q Consensus 209 ~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk 244 (280)
..-.|.+|+...-+.=+.- ......|..||.++.+
T Consensus 20 t~f~CP~Cge~~v~v~~~k-~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKK-NIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCCeEeeeecCC-CcceEECCCCCCccCE
Confidence 3567999994322211111 3447899999999876
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=49.18 E-value=12 Score=30.44 Aligned_cols=35 Identities=29% Similarity=0.602 Sum_probs=24.7
Q ss_pred CCCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhh
Q 023588 208 DTPRKCMHCEVAETPQWREGPMGPKTLCNACGVRYRS 244 (280)
Q Consensus 208 ~~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk 244 (280)
..++.|++|+... |.|-.=..| -.||-.|.-..+.
T Consensus 11 ~~N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~ 45 (116)
T PF01412_consen 11 PGNKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRS 45 (116)
T ss_dssp TTCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHH
T ss_pred cCcCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHH
Confidence 4567999999555 599888888 8999999988776
No 11
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=48.97 E-value=6.3 Score=38.29 Aligned_cols=35 Identities=31% Similarity=0.731 Sum_probs=29.4
Q ss_pred CCCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhh
Q 023588 208 DTPRKCMHCEVAETPQWREGPMGPKTLCNACGVRYRS 244 (280)
Q Consensus 208 ~~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk 244 (280)
...+.|+.|+... |+|=.=.-| -.||=-|.--.|.
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 4567899999999 999998999 8999999654443
No 12
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=47.54 E-value=4.4 Score=34.93 Aligned_cols=30 Identities=30% Similarity=0.527 Sum_probs=22.6
Q ss_pred CccCcCCCCCCCCcCCCCCCChhHhHHhhhH
Q 023588 211 RKCMHCEVAETPQWREGPMGPKTLCNACGVR 241 (280)
Q Consensus 211 ~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~ 241 (280)
..|..|+...|-.=+++- ---.-|+|||-.
T Consensus 103 VlC~~C~spdT~l~k~~r-~~~l~C~ACGa~ 132 (138)
T PRK03988 103 VICPECGSPDTKLIKEGR-IWVLKCEACGAE 132 (138)
T ss_pred EECCCCCCCCcEEEEcCC-eEEEEcccCCCC
Confidence 579999999998877522 113589999964
No 13
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.22 E-value=12 Score=39.84 Aligned_cols=36 Identities=22% Similarity=0.651 Sum_probs=29.3
Q ss_pred CCCCCccCcCCCCCCCCcCCCCCC---ChhHhHHhhhHH
Q 023588 207 TDTPRKCMHCEVAETPQWREGPMG---PKTLCNACGVRY 242 (280)
Q Consensus 207 ~~~~~~C~~Cgvt~TP~WR~GP~G---~~tLCNACGL~~ 242 (280)
.+..-.|..|.+.-||.|+.-+.+ ...+|.+|----
T Consensus 459 a~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSn 497 (706)
T KOG3740|consen 459 ATEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSN 497 (706)
T ss_pred cCCchhhhhcccccccccccccccCcchHHHHHhhhhhc
Confidence 345678999999999999987766 458999997643
No 14
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=45.68 E-value=5.1 Score=34.35 Aligned_cols=31 Identities=29% Similarity=0.587 Sum_probs=22.9
Q ss_pred CccCcCCCCCCCCcCCCCCCChhHhHHhhhHH
Q 023588 211 RKCMHCEVAETPQWREGPMGPKTLCNACGVRY 242 (280)
Q Consensus 211 ~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~ 242 (280)
..|..|+...|-+=+.+- ---.-|+|||-..
T Consensus 98 VlC~~C~sPdT~l~k~~r-~~~l~C~ACGa~~ 128 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGR-VSLLKCEACGAKA 128 (133)
T ss_pred EECCCCCCCCcEEEEeCC-eEEEecccCCCCC
Confidence 579999999998887532 1124899999653
No 15
>PF15468 DUF4636: Domain of unknown function (DUF4636)
Probab=44.94 E-value=9 Score=36.15 Aligned_cols=76 Identities=20% Similarity=0.351 Sum_probs=39.5
Q ss_pred CCCCCCCCccc-ccccCCCCCCCCCCCCCCC--CCCCCCcCCCchhhhhhhcccCCCcCCCccccccCCCCCCCCCCccC
Q 023588 138 RPATLNPLFIY-PFISSTSSTSEDYHPETAS--ESGSEMNLTEKPVRKKQKRKKNLTVLSGSRENKKLSFQQTDTPRKCM 214 (280)
Q Consensus 138 R~~~~~~~~~~-p~i~stss~~~~~~~s~~s--~Sd~E~~~~s~~~~~kKkkKrk~~lps~~v~~~~~~~~~~~~~~~C~ 214 (280)
|-+.|+.+.-. +..-+|-.-.+.+.+-+++ +|++|..++.--++++|---|...+ ..-....+.|.
T Consensus 131 ~~sqf~~~nQ~~~dsdTte~dseeSnSgAssWKesEsehhPsp~sikrrk~aqRQrn~-----------gsyqIRErPCl 199 (243)
T PF15468_consen 131 RHSQFSQVNQIQHDSDTTECDSEESNSGASSWKESESEHHPSPASIKRRKIAQRQRNL-----------GSYQIRERPCL 199 (243)
T ss_pred HHHHHHHhccccccccccccCCcccccCCccccccccccCCCchhhhhhhHHHhhccc-----------ccceeecccch
Confidence 34456544433 4444444444554444444 5666665554332321211122111 11234567899
Q ss_pred cCCCCCCCCc
Q 023588 215 HCEVAETPQW 224 (280)
Q Consensus 215 ~Cgvt~TP~W 224 (280)
||....|-+|
T Consensus 200 HCKAmRt~EW 209 (243)
T PF15468_consen 200 HCKAMRTNEW 209 (243)
T ss_pred hhHHHHHHHH
Confidence 9999999999
No 16
>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=43.38 E-value=37 Score=26.36 Aligned_cols=46 Identities=17% Similarity=0.420 Sum_probs=33.8
Q ss_pred CCCccCcCCCCCCCCc---CCCCCCChhHhHHhhhHHhhCCCCCCCCCC
Q 023588 209 TPRKCMHCEVAETPQW---REGPMGPKTLCNACGVRYRSGRLVPEYRPA 254 (280)
Q Consensus 209 ~~~~C~~Cgvt~TP~W---R~GP~G~~tLCNACGL~~kk~r~~p~yrpa 254 (280)
....|..|..+.|--= --...-+...|-+|..+|-.|+.|-....+
T Consensus 4 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvg 52 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVG 52 (63)
T ss_pred cCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccC
Confidence 4568999999887543 122345578999999999999887666443
No 17
>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=43.06 E-value=5.7 Score=29.08 Aligned_cols=25 Identities=32% Similarity=0.893 Sum_probs=18.1
Q ss_pred CCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHh
Q 023588 209 TPRKCMHCEVAETPQWREGPMGPKTLCNACGVRYR 243 (280)
Q Consensus 209 ~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~k 243 (280)
....|.+||...- +..+|.+|| +|+
T Consensus 25 ~l~~c~~cg~~~~---------~H~vc~~cG-~y~ 49 (56)
T PF01783_consen 25 NLVKCPNCGEPKL---------PHRVCPSCG-YYK 49 (56)
T ss_dssp SEEESSSSSSEES---------TTSBCTTTB-BSS
T ss_pred ceeeeccCCCEec---------ccEeeCCCC-eEC
Confidence 4568999996433 368999999 444
No 18
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=42.29 E-value=6.1 Score=32.80 Aligned_cols=29 Identities=28% Similarity=0.468 Sum_probs=21.8
Q ss_pred CccCcCCCCCCCCcCCCCCCChhHhHHhhh
Q 023588 211 RKCMHCEVAETPQWREGPMGPKTLCNACGV 240 (280)
Q Consensus 211 ~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL 240 (280)
..|..|+...|-+=+.+- ---.-|+|||-
T Consensus 81 VlC~~C~spdT~l~k~~r-~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENR-LFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCC-eEEEEccccCC
Confidence 579999999999888621 11246999995
No 19
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=40.58 E-value=16 Score=36.79 Aligned_cols=45 Identities=27% Similarity=0.595 Sum_probs=32.5
Q ss_pred CCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhh-CCCCCCCCCCC
Q 023588 209 TPRKCMHCEVAETPQWREGPMGPKTLCNACGVRYRS-GRLVPEYRPAA 255 (280)
Q Consensus 209 ~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk-~r~~p~yrpa~ 255 (280)
.++.|+.|+... |.|=.=..| -.||-.|.-..+. |-.+...|...
T Consensus 21 gNk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRsLGvHISfVRSlt 66 (395)
T PLN03114 21 DNKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRSLGVHISFVRSTN 66 (395)
T ss_pred CCCcCccCCCCC-CCceeeccc-eeehhhhhHhhccCCCCCceeeccc
Confidence 567899999875 999988888 8999999766555 32333444433
No 20
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=39.97 E-value=6.7 Score=35.30 Aligned_cols=33 Identities=24% Similarity=0.461 Sum_probs=24.5
Q ss_pred CccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhh
Q 023588 211 RKCMHCEVAETPQWREGPMGPKTLCNACGVRYRS 244 (280)
Q Consensus 211 ~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk 244 (280)
..|..|+...|-+=+.+- ---.-|+|||-..--
T Consensus 99 V~C~~C~~pdT~l~k~~~-~~~l~C~aCGa~~~v 131 (201)
T PRK12336 99 VICSECGLPDTRLVKEDR-VLMLRCDACGAHRPV 131 (201)
T ss_pred EECCCCCCCCcEEEEcCC-eEEEEcccCCCCccc
Confidence 579999999999877631 112489999987644
No 21
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=38.59 E-value=31 Score=25.92 Aligned_cols=49 Identities=29% Similarity=0.598 Sum_probs=31.3
Q ss_pred CCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhhCCCCCCCCCCCCCCccccccccchHHHHHhhh
Q 023588 209 TPRKCMHCEVAETPQWREGPMGPKTLCNACGVRYRSGRLVPEYRPAASPTFVPSLHSNSHKRIMEMRN 276 (280)
Q Consensus 209 ~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk~r~~p~yrpa~sptf~p~~~s~~h~kv~~~r~ 276 (280)
..+.|..||+... +..|-.||.. ...++.+.|.|.---..|+-.+..|.
T Consensus 4 ~mr~C~~CgvYTL----------k~~CP~CG~~---------t~~~~P~rfSp~D~y~~yR~~~kk~~ 52 (56)
T PRK13130 4 KIRKCPKCGVYTL----------KEICPVCGGK---------TKNPHPPRFSPEDKYGKYRRALKKRR 52 (56)
T ss_pred cceECCCCCCEEc----------cccCcCCCCC---------CCCCCCCCCCCCCccHHHHHHHHHHh
Confidence 4578888888665 4578888854 44556677777555555555555443
No 22
>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=36.78 E-value=11 Score=36.11 Aligned_cols=37 Identities=19% Similarity=0.492 Sum_probs=25.9
Q ss_pred CCCCCccCcCCCCCCCCc----CCCCCCCh--hHhHHhhhHHh
Q 023588 207 TDTPRKCMHCEVAETPQW----REGPMGPK--TLCNACGVRYR 243 (280)
Q Consensus 207 ~~~~~~C~~Cgvt~TP~W----R~GP~G~~--tLCNACGL~~k 243 (280)
......|..|+-...-.| |.+.++-. ..|..||-+|+
T Consensus 255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 255 VTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred CcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 345689999998776555 44444422 38999999886
No 23
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=35.92 E-value=21 Score=22.33 Aligned_cols=23 Identities=26% Similarity=0.794 Sum_probs=14.9
Q ss_pred CccCcCCCCCCCCcCCCCCCChhHhHHhhhH
Q 023588 211 RKCMHCEVAETPQWREGPMGPKTLCNACGVR 241 (280)
Q Consensus 211 ~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~ 241 (280)
+.|.+||....+. ...|-.||..
T Consensus 3 ~~Cp~Cg~~~~~~--------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPD--------AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcc--------cccChhhCCC
Confidence 4688888755433 3477777753
No 24
>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=34.65 E-value=8 Score=26.45 Aligned_cols=30 Identities=27% Similarity=0.655 Sum_probs=16.1
Q ss_pred ccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhh
Q 023588 212 KCMHCEVAETPQWREGPMGPKTLCNACGVRYRS 244 (280)
Q Consensus 212 ~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk 244 (280)
.|.+|+.+. -.+- .-.| ..+|..||+-..-
T Consensus 2 ~Cp~Cg~~~-~~~D-~~~g-~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKE-IVFD-PERG-ELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSE-EEEE-TTTT-EEEETTT-BBEE-
T ss_pred CCcCCcCCc-eEEc-CCCC-eEECCCCCCEeec
Confidence 477787765 2222 2233 5688888865543
No 25
>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=33.69 E-value=11 Score=25.66 Aligned_cols=31 Identities=29% Similarity=0.648 Sum_probs=19.9
Q ss_pred CCccCcCCCCCCCCcCCCCCCChhHhHHhhh
Q 023588 210 PRKCMHCEVAETPQWREGPMGPKTLCNACGV 240 (280)
Q Consensus 210 ~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL 240 (280)
..+|.+|++---|.-.=...|....||-|+.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCC
Confidence 4589999998888777777787889999986
No 26
>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=33.43 E-value=31 Score=27.99 Aligned_cols=34 Identities=32% Similarity=0.730 Sum_probs=28.5
Q ss_pred CCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhh
Q 023588 209 TPRKCMHCEVAETPQWREGPMGPKTLCNACGVRYRS 244 (280)
Q Consensus 209 ~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk 244 (280)
.+..|++|+. .-|+|=.=..| -.||-.|.-..+.
T Consensus 2 ~N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~ 35 (112)
T smart00105 2 GNKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRS 35 (112)
T ss_pred CCCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHh
Confidence 3578999998 45999888888 8999999877776
No 27
>PF15396 FAM60A: Protein Family FAM60A
Probab=32.95 E-value=22 Score=33.17 Aligned_cols=18 Identities=28% Similarity=0.639 Sum_probs=14.1
Q ss_pred hhHhHHhhhHHhhCCCCC
Q 023588 232 KTLCNACGVRYRSGRLVP 249 (280)
Q Consensus 232 ~tLCNACGL~~kk~r~~p 249 (280)
+.+||||=|.+++-+.||
T Consensus 49 GeICNACVLLVKRwKKLP 66 (213)
T PF15396_consen 49 GEICNACVLLVKRWKKLP 66 (213)
T ss_pred chhhHHHHHHHHHHhhCC
Confidence 469999999998844444
No 28
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=32.81 E-value=4.1 Score=27.81 Aligned_cols=32 Identities=31% Similarity=0.650 Sum_probs=19.5
Q ss_pred ccCcCCCCCCCCc----CCCCCCCh--hHhHHhhhHHh
Q 023588 212 KCMHCEVAETPQW----REGPMGPK--TLCNACGVRYR 243 (280)
Q Consensus 212 ~C~~Cgvt~TP~W----R~GP~G~~--tLCNACGL~~k 243 (280)
.|..|+-..+-.| |.+.++.. ..|..||-+|+
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 5888888764433 66666633 37989987764
No 29
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=32.69 E-value=15 Score=35.31 Aligned_cols=30 Identities=27% Similarity=0.568 Sum_probs=23.0
Q ss_pred CCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHH
Q 023588 209 TPRKCMHCEVAETPQWREGPMGPKTLCNACGVRY 242 (280)
Q Consensus 209 ~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~ 242 (280)
..+.|.+||+...+. ..|-+.+|+.||..+
T Consensus 110 ~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~ 139 (279)
T COG2816 110 SHRFCGRCGTKTYPR----EGGWARVCPKCGHEH 139 (279)
T ss_pred hCcCCCCCCCcCccc----cCceeeeCCCCCCcc
Confidence 356899999987764 346678999999764
No 30
>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=31.67 E-value=20 Score=26.13 Aligned_cols=31 Identities=23% Similarity=0.520 Sum_probs=22.8
Q ss_pred CCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHh
Q 023588 209 TPRKCMHCEVAETPQWREGPMGPKTLCNACGVRYR 243 (280)
Q Consensus 209 ~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~k 243 (280)
....|..||...-- ...+....|..||..+-
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 45689999987644 44555789999998653
No 31
>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=30.77 E-value=23 Score=24.13 Aligned_cols=26 Identities=27% Similarity=0.650 Sum_probs=20.1
Q ss_pred CCccCcCCCCCCCCcCCCCCCChhHhHHhhh
Q 023588 210 PRKCMHCEVAETPQWREGPMGPKTLCNACGV 240 (280)
Q Consensus 210 ~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL 240 (280)
...|..|+.. |-...+| ...|..||-
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 3459999987 6666678 899999984
No 32
>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=30.59 E-value=32 Score=30.86 Aligned_cols=33 Identities=21% Similarity=0.608 Sum_probs=24.1
Q ss_pred CCccCcCCCCCCCCcCC-------CCCCChhHhHHhhhHH
Q 023588 210 PRKCMHCEVAETPQWRE-------GPMGPKTLCNACGVRY 242 (280)
Q Consensus 210 ~~~C~~Cgvt~TP~WR~-------GP~G~~tLCNACGL~~ 242 (280)
+..|.+|++..--.|-- ++......|+.||..|
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 45788888877666632 4555668999999987
No 33
>COG3952 Predicted membrane protein [Function unknown]
Probab=29.02 E-value=19 Score=30.66 Aligned_cols=18 Identities=33% Similarity=0.523 Sum_probs=12.7
Q ss_pred cCCCCCCChhHhHHhhhHHh
Q 023588 224 WREGPMGPKTLCNACGVRYR 243 (280)
Q Consensus 224 WR~GP~G~~tLCNACGL~~k 243 (280)
||.+|-+ .||+|||+.-.
T Consensus 77 ~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 77 RRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HhcchHH--HHHHhhhHHHH
Confidence 4555544 79999999653
No 34
>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=28.97 E-value=11 Score=31.91 Aligned_cols=29 Identities=31% Similarity=0.612 Sum_probs=22.5
Q ss_pred CccCcCCCCCCCCcCCCCCCChhHhHHhhh
Q 023588 211 RKCMHCEVAETPQWREGPMGPKTLCNACGV 240 (280)
Q Consensus 211 ~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL 240 (280)
..|..|+...|-+=+.+..- -.-|+|||-
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 57999999999888773322 468999995
No 35
>PF14122 YokU: YokU-like protein
Probab=27.66 E-value=13 Score=30.44 Aligned_cols=33 Identities=33% Similarity=0.836 Sum_probs=22.6
Q ss_pred ccCcCCCCC-----CCCcCCCCCCCh---------hHhHHhhhHHhh
Q 023588 212 KCMHCEVAE-----TPQWREGPMGPK---------TLCNACGVRYRS 244 (280)
Q Consensus 212 ~C~~Cgvt~-----TP~WR~GP~G~~---------tLCNACGL~~kk 244 (280)
.|..|+..+ +.....=|+|.+ ..|+.||+-|..
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 488898863 333344566653 589999998865
No 36
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=27.27 E-value=30 Score=36.10 Aligned_cols=49 Identities=24% Similarity=0.520 Sum_probs=29.6
Q ss_pred CccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhhCCCCC--CCCCCCCCCcccc
Q 023588 211 RKCMHCEVAETPQWREGPMGPKTLCNACGVRYRSGRLVP--EYRPAASPTFVPS 262 (280)
Q Consensus 211 ~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk~r~~p--~yrpa~sptf~p~ 262 (280)
..|.||+.+. +. |+-..| ...|+|||.-..-....- .+--.++++||..
T Consensus 1 ~~C~~C~~s~-fe-~d~a~g-~~~C~~CG~v~E~~~ivsev~F~e~~~G~~v~~ 51 (521)
T KOG1598|consen 1 MVCKNCGGSN-FE-RDEATG-NLYCTACGTVLEYNNIVAEVTFVEGAQGQFVRV 51 (521)
T ss_pred CcCCCCCCCC-cc-cccccC-CceeccccceeeccceeEEeeeecccceeEEec
Confidence 3699999864 22 233455 789999998765533311 1111267778664
No 37
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=27.17 E-value=46 Score=27.23 Aligned_cols=31 Identities=16% Similarity=0.326 Sum_probs=23.1
Q ss_pred CCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhh
Q 023588 209 TPRKCMHCEVAETPQWREGPMGPKTLCNACGVRYRS 244 (280)
Q Consensus 209 ~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk 244 (280)
....|..|+...+-.+ .| ...|+||..+|++
T Consensus 17 ~~~~C~VCg~~a~g~h----yG-v~sC~aCk~FFRR 47 (101)
T cd07160 17 GNEVCSVCGDKASGFH----YN-VLSCEGCKGFFRR 47 (101)
T ss_pred CCCCCeecCCcCcceE----EC-cceehhhhhhhhh
Confidence 4567999997655432 34 4689999999997
No 38
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=26.82 E-value=18 Score=26.99 Aligned_cols=25 Identities=24% Similarity=0.681 Sum_probs=19.4
Q ss_pred CCCCccCcCCCCCCCCcCCCCCCChhHhHHhhhH
Q 023588 208 DTPRKCMHCEVAETPQWREGPMGPKTLCNACGVR 241 (280)
Q Consensus 208 ~~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~ 241 (280)
...-.|.+||...-| ..+|..||.|
T Consensus 25 ~~l~~C~~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 25 PGLVECPNCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred CcceECCCCCCccCC---------eEECCCCCcC
Confidence 345679999987665 6899999944
No 39
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=26.67 E-value=21 Score=24.75 Aligned_cols=27 Identities=26% Similarity=0.508 Sum_probs=19.3
Q ss_pred CccCcCCCCCCCCcCCCCCCChhHhHHhhh
Q 023588 211 RKCMHCEVAETPQWREGPMGPKTLCNACGV 240 (280)
Q Consensus 211 ~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL 240 (280)
..|-+||.+ ..-|-++ .+ ..-|++|+-
T Consensus 19 ~~CP~Cg~~-~~~~~~~-~~-~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-KHYRLKT-RG-RYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-eeEEeCC-CC-eEECCCCCC
Confidence 569999998 5555544 33 678999974
No 40
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=26.05 E-value=12 Score=29.03 Aligned_cols=35 Identities=20% Similarity=0.341 Sum_probs=26.5
Q ss_pred CCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhh
Q 023588 210 PRKCMHCEVAETPQWREGPMGPKTLCNACGVRYRS 244 (280)
Q Consensus 210 ~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk 244 (280)
+-.|-.|.+..|-+|.+...-.-.-|-+||-.-+.
T Consensus 10 GA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~~ 44 (66)
T COG3529 10 GAVCPACQAQDTLAMWRENNVEIVECVKCGHHMRE 44 (66)
T ss_pred cCCCcccchhhHHHHHHhcCCceEehhhcchHhhh
Confidence 45799999999966655444447789999987754
No 41
>PF12773 DZR: Double zinc ribbon
Probab=25.60 E-value=30 Score=23.79 Aligned_cols=30 Identities=27% Similarity=0.647 Sum_probs=19.0
Q ss_pred CCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHh
Q 023588 209 TPRKCMHCEVAETPQWREGPMGPKTLCNACGVRYR 243 (280)
Q Consensus 209 ~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~k 243 (280)
....|.+||+.-. ........|..||-.+.
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGAENP 40 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcCCCc
Confidence 4567888887766 33344567777776543
No 42
>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=25.54 E-value=28 Score=30.80 Aligned_cols=34 Identities=24% Similarity=0.433 Sum_probs=25.9
Q ss_pred ccCcCCCCCCCCc--CCCCCCC----hhHhHHhhhHHhhC
Q 023588 212 KCMHCEVAETPQW--REGPMGP----KTLCNACGVRYRSG 245 (280)
Q Consensus 212 ~C~~Cgvt~TP~W--R~GP~G~----~tLCNACGL~~kk~ 245 (280)
+|-.|+...|-.= |...+|. .--|.+||-+|-..
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTy 41 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTF 41 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcccee
Confidence 6999999888776 5556663 35899999999763
No 43
>KOG3413 consensus Mitochondrial matrix protein frataxin, involved in Fe/S protein biosynthesis [Inorganic ion transport and metabolism]
Probab=24.67 E-value=43 Score=30.02 Aligned_cols=28 Identities=21% Similarity=0.405 Sum_probs=21.6
Q ss_pred CchhHHHHhhhhhhhccCCCCcccccccc
Q 023588 11 LDEFFDDVVDTLEDLEACNIGVDDWNANF 39 (280)
Q Consensus 11 ~d~~fdd~~~~led~e~~~~~~~dw~a~~ 39 (280)
-|+.+|+|.|++||+..+-. +++.|..+
T Consensus 51 AddTLd~L~d~fEdl~e~~~-~~~~Dv~y 78 (156)
T KOG3413|consen 51 ADDTLDHLSDYFEDLAEEVP-GEGFDVDY 78 (156)
T ss_pred HHHHHHHHHHHHHHHHhhcC-cccccccc
Confidence 58889999999999987766 46666544
No 44
>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=24.16 E-value=42 Score=23.21 Aligned_cols=30 Identities=17% Similarity=0.499 Sum_probs=20.4
Q ss_pred CccCcCCCCCCCCcCCCCCCChhHhHHhhh
Q 023588 211 RKCMHCEVAETPQWREGPMGPKTLCNACGV 240 (280)
Q Consensus 211 ~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL 240 (280)
..|-.|+....=.|..-...-...|+.||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 469999988766675432222679999973
No 45
>PHA02998 RNA polymerase subunit; Provisional
Probab=23.78 E-value=22 Score=32.73 Aligned_cols=36 Identities=19% Similarity=0.503 Sum_probs=27.7
Q ss_pred CCCccCcCCCCCCCCc----CCCCCCCh--hHhHHhhhHHhh
Q 023588 209 TPRKCMHCEVAETPQW----REGPMGPK--TLCNACGVRYRS 244 (280)
Q Consensus 209 ~~~~C~~Cgvt~TP~W----R~GP~G~~--tLCNACGL~~kk 244 (280)
....|..|+-..+--| |.+.++.- ..|-.||-+|+-
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 4468999998886655 87877733 389999999974
No 46
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=23.42 E-value=28 Score=35.99 Aligned_cols=32 Identities=22% Similarity=0.459 Sum_probs=22.3
Q ss_pred CCccCcCCCCC-CCCcCCCCCCCh----------hHhHHhhhH
Q 023588 210 PRKCMHCEVAE-TPQWREGPMGPK----------TLCNACGVR 241 (280)
Q Consensus 210 ~~~C~~Cgvt~-TP~WR~GP~G~~----------tLCNACGL~ 241 (280)
...|.+||... +++=+.+|.+.. +.||+||--
T Consensus 161 ~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~ 203 (500)
T KOG0909|consen 161 NPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTE 203 (500)
T ss_pred CCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCc
Confidence 34799999876 555555555433 689999963
No 47
>PRK00420 hypothetical protein; Validated
Probab=22.34 E-value=27 Score=29.40 Aligned_cols=30 Identities=23% Similarity=0.557 Sum_probs=22.6
Q ss_pred CCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhh
Q 023588 210 PRKCMHCEVAETPQWREGPMGPKTLCNACGVRYRS 244 (280)
Q Consensus 210 ~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk 244 (280)
...|..|| +|+.|- .+| +..|-+||..+..
T Consensus 23 ~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCC---Ccceec-CCC-ceECCCCCCeeee
Confidence 35688888 788874 355 8999999987654
No 48
>PLN03131 hypothetical protein; Provisional
Probab=22.19 E-value=42 Score=36.06 Aligned_cols=34 Identities=24% Similarity=0.533 Sum_probs=26.9
Q ss_pred CCCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHh
Q 023588 208 DTPRKCMHCEVAETPQWREGPMGPKTLCNACGVRYR 243 (280)
Q Consensus 208 ~~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~k 243 (280)
..+++|++|+... |.|-.-..| -.||-.|.=..+
T Consensus 21 PgNk~CADCga~~-P~WASiNlG-IFICi~CSGIHR 54 (705)
T PLN03131 21 PPNRRCINCNSLG-PQFVCTNFW-TFICMTCSGIHR 54 (705)
T ss_pred cCCCccccCCCCC-CCeeEeccc-eEEchhchhhhc
Confidence 4567999999765 999887788 789999965443
No 49
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=21.89 E-value=33 Score=30.38 Aligned_cols=29 Identities=21% Similarity=0.607 Sum_probs=23.7
Q ss_pred CCccCcCCCCCCCCcCCCCCCChhHhHHhh
Q 023588 210 PRKCMHCEVAETPQWREGPMGPKTLCNACG 239 (280)
Q Consensus 210 ~~~C~~Cgvt~TP~WR~GP~G~~tLCNACG 239 (280)
...|..||......|-.-.+| +.+|..|+
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 358999998877677766777 89999997
No 50
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=21.43 E-value=59 Score=31.10 Aligned_cols=30 Identities=27% Similarity=0.526 Sum_probs=19.9
Q ss_pred CccCcCCCCCC-CCcCCCCCCChhHhHHhhhHHh
Q 023588 211 RKCMHCEVAET-PQWREGPMGPKTLCNACGVRYR 243 (280)
Q Consensus 211 ~~C~~Cgvt~T-P~WR~GP~G~~tLCNACGL~~k 243 (280)
+.|..|.-..| |-=.=..+| +||+|-.+-.
T Consensus 2 ~~C~~C~~~~t~p~i~fd~~G---vC~~C~~~~~ 32 (343)
T TIGR03573 2 KFCKRCVMPTTRPGITFDEDG---VCSACRNFEE 32 (343)
T ss_pred CcCCCCCCCCCCCCeeECCCC---CchhhhhHHh
Confidence 47999988765 322334455 8999988653
No 51
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=21.28 E-value=18 Score=24.82 Aligned_cols=32 Identities=28% Similarity=0.648 Sum_probs=20.4
Q ss_pred ccCcCCCCCCCCc----CCCCCCCh--hHhHHhhhHHh
Q 023588 212 KCMHCEVAETPQW----REGPMGPK--TLCNACGVRYR 243 (280)
Q Consensus 212 ~C~~Cgvt~TP~W----R~GP~G~~--tLCNACGL~~k 243 (280)
.|-+|+-.+.--| |.+.++.. ..|-.||-+|+
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 5888886654333 66666633 37888887765
No 52
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=20.92 E-value=42 Score=35.77 Aligned_cols=34 Identities=26% Similarity=0.555 Sum_probs=26.9
Q ss_pred CCCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHh
Q 023588 208 DTPRKCMHCEVAETPQWREGPMGPKTLCNACGVRYR 243 (280)
Q Consensus 208 ~~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~k 243 (280)
..++.|++|+... |.|=.-..| -.+|-.|.=-.+
T Consensus 21 PgNk~CADCgs~~-P~WASiNlG-IFICi~CSGIHR 54 (648)
T PLN03119 21 PPNRRCINCNSLG-PQYVCTTFW-TFVCMACSGIHR 54 (648)
T ss_pred cCCCccccCCCCC-CCceeeccc-eEEeccchhhhc
Confidence 4567999999876 999887788 789999964433
No 53
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.84 E-value=37 Score=32.09 Aligned_cols=11 Identities=27% Similarity=0.924 Sum_probs=5.1
Q ss_pred hhHhHHhhhHH
Q 023588 232 KTLCNACGVRY 242 (280)
Q Consensus 232 ~tLCNACGL~~ 242 (280)
.++|.-||+-+
T Consensus 30 e~vC~~CG~Vl 40 (310)
T PRK00423 30 EIVCADCGLVI 40 (310)
T ss_pred eEeecccCCcc
Confidence 44455554433
No 54
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=20.36 E-value=28 Score=32.24 Aligned_cols=29 Identities=28% Similarity=0.474 Sum_probs=20.7
Q ss_pred CCCccCcCCCCCCCCcCCCCCCChhHhHHhhhH
Q 023588 209 TPRKCMHCEVAETPQWREGPMGPKTLCNACGVR 241 (280)
Q Consensus 209 ~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~ 241 (280)
..+.|.+||...... ..|....|.+||..
T Consensus 98 ~~~fC~~CG~~~~~~----~~~~~~~C~~c~~~ 126 (256)
T PRK00241 98 SHRFCGYCGHPMHPS----KTEWAMLCPHCRER 126 (256)
T ss_pred cCccccccCCCCeec----CCceeEECCCCCCE
Confidence 356899999875432 35667789999953
No 55
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=20.26 E-value=63 Score=25.72 Aligned_cols=31 Identities=23% Similarity=0.520 Sum_probs=23.5
Q ss_pred CCCccCcCCCCCCCCcCCCCCCChhHhHHhhhHHhh
Q 023588 209 TPRKCMHCEVAETPQWREGPMGPKTLCNACGVRYRS 244 (280)
Q Consensus 209 ~~~~C~~Cgvt~TP~WR~GP~G~~tLCNACGL~~kk 244 (280)
....|..|+...+-.+ .| ...|+||..+|++
T Consensus 5 ~~~~C~VCg~~a~g~h----yG-v~sC~aCk~FFRR 35 (90)
T cd07169 5 EQRTCLICGDRATGLH----YG-IISCEGCKGFFKR 35 (90)
T ss_pred cCCCCeecCCcCcceE----EC-cceehhhHHHHHH
Confidence 4456999998665544 34 4689999999988
Done!