Query 047722
Match_columns 138
No_of_seqs 136 out of 725
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 02:28:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047722.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047722hhsearch_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 99.7 5.7E-17 1.2E-21 105.8 3.5 51 80-132 1-51 (54)
2 smart00401 ZnF_GATA zinc finge 99.6 4.1E-16 9E-21 100.8 2.7 44 77-122 2-46 (52)
3 PF00320 GATA: GATA zinc finge 99.6 5.8E-16 1.3E-20 93.3 1.3 35 81-117 1-35 (36)
4 KOG1601 GATA-4/5/6 transcripti 98.8 1.4E-09 3.1E-14 83.4 2.4 50 78-130 199-248 (340)
5 COG5641 GAT1 GATA Zn-finger-co 98.4 2.1E-07 4.6E-12 83.5 4.1 40 77-119 157-201 (498)
6 COG5641 GAT1 GATA Zn-finger-co 85.3 0.3 6.5E-06 44.5 0.4 43 79-123 298-341 (498)
7 KOG3554 Histone deacetylase co 70.5 3.7 8E-05 37.9 2.7 38 78-117 386-425 (693)
8 PF14803 Nudix_N_2: Nudix N-te 65.5 1.3 2.8E-05 26.3 -0.9 29 79-109 1-29 (34)
9 PRK03988 translation initiatio 58.9 2.5 5.4E-05 32.3 -0.5 28 80-110 104-131 (138)
10 TIGR00311 aIF-2beta translatio 57.2 2.9 6.2E-05 31.8 -0.5 28 80-110 99-126 (133)
11 smart00653 eIF2B_5 domain pres 57.2 3 6.5E-05 30.6 -0.3 28 80-110 82-109 (110)
12 PF01412 ArfGap: Putative GTPa 55.9 13 0.00029 26.8 2.9 38 76-117 11-48 (116)
13 COG3952 Predicted membrane pro 55.2 3.5 7.7E-05 30.7 -0.3 20 93-114 76-95 (113)
14 KOG3740 Uncharacterized conser 50.1 9 0.0002 36.3 1.5 37 74-112 458-497 (706)
15 PRK12336 translation initiatio 49.5 4.3 9.4E-05 32.5 -0.6 33 80-115 100-132 (201)
16 PF01873 eIF-5_eIF-2B: Domain 42.0 6.7 0.00014 29.4 -0.6 27 80-109 95-121 (125)
17 smart00105 ArfGap Putative GTP 41.8 25 0.00054 25.3 2.4 37 77-117 2-38 (112)
18 COG5347 GTPase-activating prot 41.1 13 0.00028 32.1 1.0 39 75-117 17-55 (319)
19 PF06677 Auto_anti-p27: Sjogre 37.2 12 0.00025 23.1 0.1 24 79-109 18-41 (41)
20 PRK12286 rpmF 50S ribosomal pr 33.3 19 0.0004 23.6 0.6 27 74-111 23-49 (57)
21 COG3529 Predicted nucleic-acid 32.2 9.9 0.00022 25.8 -0.9 33 79-114 11-44 (66)
22 cd07160 NR_DBD_LXR DNA-binding 28.4 60 0.0013 23.4 2.6 33 78-117 18-50 (101)
23 cd07173 NR_DBD_AR DNA-binding 28.4 60 0.0013 22.4 2.5 33 78-117 3-35 (82)
24 cd07169 NR_DBD_GCNF_like DNA-b 28.0 59 0.0013 22.8 2.4 34 77-117 5-38 (90)
25 PF01783 Ribosomal_L32p: Ribos 27.5 7.9 0.00017 25.0 -1.9 27 77-115 25-51 (56)
26 cd07172 NR_DBD_GR_PR DNA-bindi 27.5 51 0.0011 22.5 2.0 33 79-118 3-35 (78)
27 PF12553 DUF3742: Protein of u 26.4 24 0.00052 23.0 0.2 9 92-100 34-42 (54)
28 PF08271 TF_Zn_Ribbon: TFIIB z 26.0 19 0.00041 21.6 -0.3 26 81-111 3-28 (43)
29 PF13045 DUF3905: Protein of u 26.0 35 0.00076 24.2 0.9 18 3-20 42-59 (84)
30 PLN03114 ADP-ribosylation fact 25.3 47 0.001 29.7 1.8 38 76-117 20-57 (395)
31 cd07168 NR_DBD_DHR4_like DNA-b 22.5 88 0.0019 21.8 2.5 33 78-117 6-38 (90)
32 PF06689 zf-C4_ClpX: ClpX C4-t 22.2 37 0.00081 20.5 0.5 34 79-115 2-37 (41)
33 PF02701 zf-Dof: Dof domain, z 21.2 1.6E+02 0.0034 20.0 3.3 43 77-121 4-49 (63)
34 PF04810 zf-Sec23_Sec24: Sec23 20.6 36 0.00077 20.3 0.1 31 78-110 2-32 (40)
35 PF15396 FAM60A: Protein Famil 20.3 62 0.0013 26.7 1.5 18 101-118 48-65 (213)
36 PF06869 DUF1258: Protein of u 20.2 43 0.00093 28.4 0.6 17 95-111 11-27 (258)
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=99.66 E-value=5.7e-17 Score=105.76 Aligned_cols=51 Identities=43% Similarity=0.959 Sum_probs=43.5
Q ss_pred cccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhhhcccchhhhhccccccc
Q 047722 80 RCTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKEEEKRKAKETETSNIDQN 132 (138)
Q Consensus 80 ~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~~~~r~~~~~~~~~~~~~ 132 (138)
.|+ +|++++||+||+||.+...|||||||||++++..|+........+..+
T Consensus 1 ~C~--~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~~~~~~~~ 51 (54)
T cd00202 1 ACS--NCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRKKDQIKRR 51 (54)
T ss_pred CCC--CCCCCCCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCcccccccc
Confidence 488 999999999999998889999999999999999888877664444433
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.60 E-value=4.1e-16 Score=100.79 Aligned_cols=44 Identities=52% Similarity=1.114 Sum_probs=39.1
Q ss_pred CCccccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhhhcc-cchh
Q 047722 77 PYKRCTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKEEEK-RKAK 122 (138)
Q Consensus 77 ~~~~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~~~~-r~~~ 122 (138)
....|+ +|++++||+||+||.|...|||||||||+++..+ |+..
T Consensus 2 ~~~~C~--~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~ 46 (52)
T smart00401 2 SGRSCS--NCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLS 46 (52)
T ss_pred CCCCcC--CCCCCCCCccccCCCCCCcEeecccHHHHHcCCCCCccc
Confidence 356799 9999999999999999889999999999999987 4443
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=99.57 E-value=5.8e-16 Score=93.29 Aligned_cols=35 Identities=60% Similarity=1.342 Sum_probs=28.5
Q ss_pred ccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhhhc
Q 047722 81 CTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKEEE 117 (138)
Q Consensus 81 C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~~~ 117 (138)
|+ +|++++||+||+||.|..+|||||||+|+++++
T Consensus 1 C~--~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CS--NCGTTETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -T--TT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred Cc--CCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 67 999999999999999988899999999999976
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.84 E-value=1.4e-09 Score=83.44 Aligned_cols=50 Identities=46% Similarity=1.090 Sum_probs=41.0
Q ss_pred CccccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhhhcccchhhhhccccc
Q 047722 78 YKRCTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKEEEKRKAKETETSNID 130 (138)
Q Consensus 78 ~~~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~~~~r~~~~~~~~~~~ 130 (138)
...|. +|+++.||+||+++.|++.+||||||+|+++. .++........+.
T Consensus 199 ~~~c~--~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~-~~r~~~~~~~~~~ 248 (340)
T KOG1601|consen 199 LRQCS--NCGTTKTPLWRRGPEGPKSLCNACGLRYKKGG-VRRPLPEKRPASS 248 (340)
T ss_pred CcccC--CCCCCCCcceecCCCCCccccccchhhhhhcC-ccccccccCcccc
Confidence 47898 99999999999999999999999999999998 3444444444333
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.41 E-value=2.1e-07 Score=83.50 Aligned_cols=40 Identities=43% Similarity=0.967 Sum_probs=37.0
Q ss_pred CCccccCCCCCCCCCCccccCCC-----CCcchhhHHHHHHHhhhccc
Q 047722 77 PYKRCTNYNCNTNDTPMWRRGPL-----GPKTLCNACGIKYRKEEEKR 119 (138)
Q Consensus 77 ~~~~C~~~~C~t~~TP~WRrGp~-----G~~~LCNACGL~~~k~~~~r 119 (138)
...+|. +|.++.||+|||+.. | -.|||||||+|+-|+..|
T Consensus 157 ~~~vc~--Nc~t~stPlwrR~~~~~s~~~-n~lcnaCgl~~klhg~~r 201 (498)
T COG5641 157 QPHVCS--NCKTTSTPLWRRASSESSLPG-NNLCNACGLYLKLHGSPR 201 (498)
T ss_pred ccchhc--cccccCCccccccccccccCC-ccccccccccccccCCcC
Confidence 445899 999999999999999 6 899999999999999988
No 6
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=85.29 E-value=0.3 Score=44.46 Aligned_cols=43 Identities=30% Similarity=0.474 Sum_probs=34.9
Q ss_pred ccccCCCCCC-CCCCccccCCCCCcchhhHHHHHHHhhhcccchhh
Q 047722 79 KRCTNYNCNT-NDTPMWRRGPLGPKTLCNACGIKYRKEEEKRKAKE 123 (138)
Q Consensus 79 ~~C~~~~C~t-~~TP~WRrGp~G~~~LCNACGL~~~k~~~~r~~~~ 123 (138)
..|. +|.+ +.||.||+...---++|||||++.+..+.+++...
T Consensus 298 ~~~s--~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~p 341 (498)
T COG5641 298 KKRS--TLTTSTATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLP 341 (498)
T ss_pred cCcc--cccccccCcccccccccccccccccccccCCcccccccCC
Confidence 4466 5554 67899988876668999999999999999888766
No 7
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=70.45 E-value=3.7 Score=37.92 Aligned_cols=38 Identities=26% Similarity=0.544 Sum_probs=31.8
Q ss_pred CccccCCCCCCCCCCcc--ccCCCCCcchhhHHHHHHHhhhc
Q 047722 78 YKRCTNYNCNTNDTPMW--RRGPLGPKTLCNACGIKYRKEEE 117 (138)
Q Consensus 78 ~~~C~~~~C~t~~TP~W--RrGp~G~~~LCNACGL~~~k~~~ 117 (138)
.+.|. +|+|++.-.| .-+|.-..-||-.|=+||+|-+.
T Consensus 386 g~~CE--sC~ttqs~qWYsWGppnmqcrLCasCWiyWKKygG 425 (693)
T KOG3554|consen 386 GRACE--SCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYGG 425 (693)
T ss_pred CCccc--ccccccccceeccCCCCccchhhHHHHHHHHHhcC
Confidence 56799 9999999999 34555567899999999999874
No 8
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=65.49 E-value=1.3 Score=26.34 Aligned_cols=29 Identities=28% Similarity=0.551 Sum_probs=14.7
Q ss_pred ccccCCCCCCCCCCccccCCCCCcchhhHHH
Q 047722 79 KRCTNYNCNTNDTPMWRRGPLGPKTLCNACG 109 (138)
Q Consensus 79 ~~C~~~~C~t~~TP~WRrGp~G~~~LCNACG 109 (138)
+.|. .|+..-+-.--.|.+-.+.+|.+||
T Consensus 1 kfC~--~CG~~l~~~ip~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 1 KFCP--QCGGPLERRIPEGDDRERLVCPACG 29 (34)
T ss_dssp -B-T--TT--B-EEE--TT-SS-EEEETTTT
T ss_pred Cccc--cccChhhhhcCCCCCccceECCCCC
Confidence 4687 8887643333356666789999998
No 9
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=58.92 E-value=2.5 Score=32.29 Aligned_cols=28 Identities=32% Similarity=0.771 Sum_probs=22.3
Q ss_pred cccCCCCCCCCCCccccCCCCCcchhhHHHH
Q 047722 80 RCTNYNCNTNDTPMWRRGPLGPKTLCNACGI 110 (138)
Q Consensus 80 ~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL 110 (138)
.|. .|+..+|-+-+++-.- -..|+|||-
T Consensus 104 lC~--~C~spdT~l~k~~r~~-~l~C~ACGa 131 (138)
T PRK03988 104 ICP--ECGSPDTKLIKEGRIW-VLKCEACGA 131 (138)
T ss_pred ECC--CCCCCCcEEEEcCCeE-EEEcccCCC
Confidence 498 9999999998764433 578999994
No 10
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=57.19 E-value=2.9 Score=31.78 Aligned_cols=28 Identities=36% Similarity=0.816 Sum_probs=21.7
Q ss_pred cccCCCCCCCCCCccccCCCCCcchhhHHHH
Q 047722 80 RCTNYNCNTNDTPMWRRGPLGPKTLCNACGI 110 (138)
Q Consensus 80 ~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL 110 (138)
.|. .|+..+|-+-+.+-.- -.-|+|||-
T Consensus 99 lC~--~C~sPdT~l~k~~r~~-~l~C~ACGa 126 (133)
T TIGR00311 99 ICR--ECNRPDTRIIKEGRVS-LLKCEACGA 126 (133)
T ss_pred ECC--CCCCCCcEEEEeCCeE-EEecccCCC
Confidence 488 9999999998764322 458999994
No 11
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=57.16 E-value=3 Score=30.65 Aligned_cols=28 Identities=32% Similarity=0.682 Sum_probs=21.9
Q ss_pred cccCCCCCCCCCCccccCCCCCcchhhHHHH
Q 047722 80 RCTNYNCNTNDTPMWRRGPLGPKTLCNACGI 110 (138)
Q Consensus 80 ~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL 110 (138)
.|. .|+..+|-+-+.+-.- -.-|+|||-
T Consensus 82 lC~--~C~spdT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 82 LCP--ECGSPDTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred ECC--CCCCCCcEEEEeCCeE-EEEccccCC
Confidence 498 9999999999873332 456999994
No 12
>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=55.91 E-value=13 Score=26.82 Aligned_cols=38 Identities=26% Similarity=0.488 Sum_probs=27.4
Q ss_pred CCCccccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhhhc
Q 047722 76 YPYKRCTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKEEE 117 (138)
Q Consensus 76 ~~~~~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~~~ 117 (138)
.+.+.|+ .|+... |.|-.=..| ..||-.|.-.++..++
T Consensus 11 ~~N~~Ca--DCg~~~-p~w~s~~~G-iflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 11 PGNKVCA--DCGAPN-PTWASLNYG-IFLCLECAGIHRSLGV 48 (116)
T ss_dssp TTCTB-T--TT-SBS---EEETTTT-EEE-HHHHHHHHHHTT
T ss_pred cCcCcCC--CCCCCC-CCEEEeecC-hhhhHHHHHHHHHhcc
Confidence 4668899 998655 699998999 9999999988888763
No 13
>COG3952 Predicted membrane protein [Function unknown]
Probab=55.23 E-value=3.5 Score=30.75 Aligned_cols=20 Identities=30% Similarity=0.493 Sum_probs=14.9
Q ss_pred ccccCCCCCcchhhHHHHHHHh
Q 047722 93 MWRRGPLGPKTLCNACGIKYRK 114 (138)
Q Consensus 93 ~WRrGp~G~~~LCNACGL~~~k 114 (138)
+||.+|-+ .||+|||++-.-
T Consensus 76 i~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHhcchHH--HHHHhhhHHHHH
Confidence 46666665 799999998654
No 14
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=50.12 E-value=9 Score=36.29 Aligned_cols=37 Identities=22% Similarity=0.538 Sum_probs=29.5
Q ss_pred CCCCCccccCCCCCCCCCCccccCCCC---CcchhhHHHHHH
Q 047722 74 HGYPYKRCTNYNCNTNDTPMWRRGPLG---PKTLCNACGIKY 112 (138)
Q Consensus 74 ~~~~~~~C~~~~C~t~~TP~WRrGp~G---~~~LCNACGL~~ 112 (138)
...++-.|. .|.+.-||.|+.-+.+ .+.+|.+|----
T Consensus 458 ~a~~P~~ca--qcktdftp~wk~ekstq~d~~i~cE~cvtSn 497 (706)
T KOG3740|consen 458 LATEPYACA--QCKTDFTPAWKKEKSTQADAAIVCENCVTSN 497 (706)
T ss_pred ccCCchhhh--hcccccccccccccccCcchHHHHHhhhhhc
Confidence 444567899 9999999999987776 568999996543
No 15
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=49.53 E-value=4.3 Score=32.48 Aligned_cols=33 Identities=24% Similarity=0.539 Sum_probs=24.7
Q ss_pred cccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhh
Q 047722 80 RCTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKE 115 (138)
Q Consensus 80 ~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~ 115 (138)
.|. .|+..+|-+-+.+..- -.-|+|||-..--.
T Consensus 100 ~C~--~C~~pdT~l~k~~~~~-~l~C~aCGa~~~v~ 132 (201)
T PRK12336 100 ICS--ECGLPDTRLVKEDRVL-MLRCDACGAHRPVK 132 (201)
T ss_pred ECC--CCCCCCcEEEEcCCeE-EEEcccCCCCcccc
Confidence 498 9999999998764332 46899999765443
No 16
>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=41.96 E-value=6.7 Score=29.41 Aligned_cols=27 Identities=37% Similarity=0.801 Sum_probs=22.8
Q ss_pred cccCCCCCCCCCCccccCCCCCcchhhHHH
Q 047722 80 RCTNYNCNTNDTPMWRRGPLGPKTLCNACG 109 (138)
Q Consensus 80 ~C~~~~C~t~~TP~WRrGp~G~~~LCNACG 109 (138)
.|. .|+..+|-+-+.+..- -.-|+|||
T Consensus 95 lC~--~C~spdT~l~k~~r~~-~l~C~aCG 121 (125)
T PF01873_consen 95 LCP--ECGSPDTELIKEGRLI-FLKCKACG 121 (125)
T ss_dssp SCT--STSSSSEEEEEETTCC-EEEETTTS
T ss_pred EcC--CCCCCccEEEEcCCEE-EEEecccC
Confidence 487 9999999998885555 78899998
No 17
>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=41.77 E-value=25 Score=25.30 Aligned_cols=37 Identities=30% Similarity=0.582 Sum_probs=31.1
Q ss_pred CCccccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhhhc
Q 047722 77 PYKRCTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKEEE 117 (138)
Q Consensus 77 ~~~~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~~~ 117 (138)
..+.|+ +|+.. -|.|-.=..| ..||-.|.-..+..+.
T Consensus 2 ~N~~Ca--DC~~~-~p~w~s~~~G-ifvC~~CsgiHR~lg~ 38 (112)
T smart00105 2 GNKKCF--DCGAP-NPTWASVNLG-VFLCIECSGIHRSLGV 38 (112)
T ss_pred CCCccc--CCCCC-CCCcEEeccc-eeEhHHhHHHHHhcCC
Confidence 457899 99984 5999998899 9999999988887764
No 18
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=41.12 E-value=13 Score=32.13 Aligned_cols=39 Identities=28% Similarity=0.594 Sum_probs=32.9
Q ss_pred CCCCccccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhhhc
Q 047722 75 GYPYKRCTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKEEE 117 (138)
Q Consensus 75 ~~~~~~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~~~ 117 (138)
....+.|. .|++.. |.|-.=..| ..||--|.=-.+..++
T Consensus 17 ~~~Nk~Ca--DCga~~-P~W~S~nlG-vfiCi~CagvHRsLGv 55 (319)
T COG5347 17 DSSNKKCA--DCGAPN-PTWASVNLG-VFLCIDCAGVHRSLGV 55 (319)
T ss_pred ccccCccc--cCCCCC-CceEecccC-eEEEeecchhhhcccc
Confidence 34667898 999999 999999999 9999999776666654
No 19
>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=37.16 E-value=12 Score=23.06 Aligned_cols=24 Identities=42% Similarity=1.068 Sum_probs=17.8
Q ss_pred ccccCCCCCCCCCCccccCCCCCcchhhHHH
Q 047722 79 KRCTNYNCNTNDTPMWRRGPLGPKTLCNACG 109 (138)
Q Consensus 79 ~~C~~~~C~t~~TP~WRrGp~G~~~LCNACG 109 (138)
..|. .| .+|+.| ...| ..+|-+|+
T Consensus 18 ~~Cp--~C---~~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCP--DC---GTPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred CccC--CC---CCeeEE-ecCC-CEECCCCC
Confidence 3476 67 599999 3466 78999885
No 20
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=33.26 E-value=19 Score=23.57 Aligned_cols=27 Identities=26% Similarity=0.709 Sum_probs=19.1
Q ss_pred CCCCCccccCCCCCCCCCCccccCCCCCcchhhHHHHH
Q 047722 74 HGYPYKRCTNYNCNTNDTPMWRRGPLGPKTLCNACGIK 111 (138)
Q Consensus 74 ~~~~~~~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~ 111 (138)
.....-.|. +||...-| +.+|..||.|
T Consensus 23 ~~~~l~~C~--~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 23 KAPGLVECP--NCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred cCCcceECC--CCCCccCC---------eEECCCCCcC
Confidence 334456698 89866544 8899999954
No 21
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=32.16 E-value=9.9 Score=25.82 Aligned_cols=33 Identities=30% Similarity=0.733 Sum_probs=24.6
Q ss_pred ccccCCCCCCCCCCc-cccCCCCCcchhhHHHHHHHh
Q 047722 79 KRCTNYNCNTNDTPM-WRRGPLGPKTLCNACGIKYRK 114 (138)
Q Consensus 79 ~~C~~~~C~t~~TP~-WRrGp~G~~~LCNACGL~~~k 114 (138)
..|- .|.+.+|=. ||.+.-. ...|-+||-.-+.
T Consensus 11 A~CP--~C~~~Dtl~mW~En~ve-~vECV~CG~~~~~ 44 (66)
T COG3529 11 AVCP--ACQAQDTLAMWRENNVE-IVECVKCGHHMRE 44 (66)
T ss_pred CCCc--ccchhhHHHHHHhcCCc-eEehhhcchHhhh
Confidence 4587 999999954 5655444 8899999987643
No 22
>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=28.42 E-value=60 Score=23.38 Aligned_cols=33 Identities=15% Similarity=0.411 Sum_probs=24.5
Q ss_pred CccccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhhhc
Q 047722 78 YKRCTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKEEE 117 (138)
Q Consensus 78 ~~~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~~~ 117 (138)
...|. -|+...+-.+ .| ...|+||..||++...
T Consensus 18 ~~~C~--VCg~~a~g~h----yG-v~sC~aCk~FFRR~v~ 50 (101)
T cd07160 18 NEVCS--VCGDKASGFH----YN-VLSCEGCKGFFRRSVI 50 (101)
T ss_pred CCCCe--ecCCcCcceE----EC-cceehhhhhhhhhccc
Confidence 44588 8987555332 45 6889999999998875
No 23
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) 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. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=28.36 E-value=60 Score=22.40 Aligned_cols=33 Identities=21% Similarity=0.609 Sum_probs=24.0
Q ss_pred CccccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhhhc
Q 047722 78 YKRCTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKEEE 117 (138)
Q Consensus 78 ~~~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~~~ 117 (138)
.+.|. .|+...+-.+ .| ...|+||..||++...
T Consensus 3 ~~~C~--VCg~~a~g~h----yG-v~sC~aCk~FFRR~v~ 35 (82)
T cd07173 3 QKTCL--ICGDEASGCH----YG-ALTCGSCKVFFKRAAE 35 (82)
T ss_pred CCCCe--ecCCcCcceE----EC-cchhhhHHHHHHHHhc
Confidence 34588 8886554332 45 6789999999999875
No 24
>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=27.98 E-value=59 Score=22.78 Aligned_cols=34 Identities=18% Similarity=0.440 Sum_probs=25.4
Q ss_pred CCccccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhhhc
Q 047722 77 PYKRCTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKEEE 117 (138)
Q Consensus 77 ~~~~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~~~ 117 (138)
....|. -|+...+-.+ .| ...|+||..||++...
T Consensus 5 ~~~~C~--VCg~~a~g~h----yG-v~sC~aCk~FFRR~v~ 38 (90)
T cd07169 5 EQRTCL--ICGDRATGLH----YG-IISCEGCKGFFKRSIC 38 (90)
T ss_pred cCCCCe--ecCCcCcceE----EC-cceehhhHHHHHHHhc
Confidence 445688 8887655544 45 6889999999999875
No 25
>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=27.53 E-value=7.9 Score=24.96 Aligned_cols=27 Identities=30% Similarity=0.829 Sum_probs=18.3
Q ss_pred CCccccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhh
Q 047722 77 PYKRCTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKE 115 (138)
Q Consensus 77 ~~~~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~ 115 (138)
....|. +|+.. .-++.+|.+|| ||+..
T Consensus 25 ~l~~c~--~cg~~---------~~~H~vc~~cG-~y~~r 51 (56)
T PF01783_consen 25 NLVKCP--NCGEP---------KLPHRVCPSCG-YYKGR 51 (56)
T ss_dssp SEEESS--SSSSE---------ESTTSBCTTTB-BSSSS
T ss_pred ceeeec--cCCCE---------ecccEeeCCCC-eECCE
Confidence 446788 88852 23479999999 55443
No 26
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=27.52 E-value=51 Score=22.45 Aligned_cols=33 Identities=21% Similarity=0.572 Sum_probs=23.2
Q ss_pred ccccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhhhcc
Q 047722 79 KRCTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKEEEK 118 (138)
Q Consensus 79 ~~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~~~~ 118 (138)
..|. -|+...+-.+ .| ...|+||..||++....
T Consensus 3 ~~C~--VCg~~a~g~h----yG-v~sC~aC~~FFRR~v~~ 35 (78)
T cd07172 3 KICL--VCSDEASGCH----YG-VLTCGSCKVFFKRAVEG 35 (78)
T ss_pred CCCe--ecCCcCcceE----EC-ceeehhhHHhHHHHeeC
Confidence 3477 7875444332 44 67899999999998753
No 27
>PF12553 DUF3742: Protein of unknown function (DUF3742); InterPro: IPR022213 This domain family is found in bacteria, and is approximately 50 amino acids in length. There is a single completely conserved residue Y that may be functionally important.
Probab=26.39 E-value=24 Score=22.97 Aligned_cols=9 Identities=67% Similarity=1.645 Sum_probs=8.4
Q ss_pred CccccCCCC
Q 047722 92 PMWRRGPLG 100 (138)
Q Consensus 92 P~WRrGp~G 100 (138)
|+||.||.|
T Consensus 34 ~E~R~G~~G 42 (54)
T PF12553_consen 34 PEWREGPAG 42 (54)
T ss_pred HhheecCCC
Confidence 899999997
No 28
>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=25.98 E-value=19 Score=21.58 Aligned_cols=26 Identities=27% Similarity=0.797 Sum_probs=14.4
Q ss_pred ccCCCCCCCCCCccccCCCCCcchhhHHHHH
Q 047722 81 CTNYNCNTNDTPMWRRGPLGPKTLCNACGIK 111 (138)
Q Consensus 81 C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~ 111 (138)
|- +|++.. .--.-..| ..+|..||+-
T Consensus 3 Cp--~Cg~~~--~~~D~~~g-~~vC~~CG~V 28 (43)
T PF08271_consen 3 CP--NCGSKE--IVFDPERG-ELVCPNCGLV 28 (43)
T ss_dssp BT--TTSSSE--EEEETTTT-EEEETTT-BB
T ss_pred Cc--CCcCCc--eEEcCCCC-eEECCCCCCE
Confidence 65 777755 22223344 6788888864
No 29
>PF13045 DUF3905: Protein of unknown function (DUF3905)
Probab=25.95 E-value=35 Score=24.22 Aligned_cols=18 Identities=33% Similarity=0.462 Sum_probs=16.8
Q ss_pred CCCCCCCCCCCCccCCCC
Q 047722 3 SQLPNSPLNYNNVSINPD 20 (138)
Q Consensus 3 ~~~~~~~m~~~~~~~~p~ 20 (138)
|-||||++++=+.-+||+
T Consensus 42 Y~S~~SPL~~WS~~~DPa 59 (84)
T PF13045_consen 42 YNSPNSPLENWSDETDPA 59 (84)
T ss_pred cCCCCCchhhcccccChh
Confidence 679999999999999998
No 30
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=25.29 E-value=47 Score=29.71 Aligned_cols=38 Identities=29% Similarity=0.576 Sum_probs=31.2
Q ss_pred CCCccccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhhhc
Q 047722 76 YPYKRCTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKEEE 117 (138)
Q Consensus 76 ~~~~~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~~~ 117 (138)
...+.|. .|+... |.|-.=..| ..||..|.=..+..++
T Consensus 20 PgNk~Ca--DCga~n-PtWASvn~G-IFLCl~CSGVHRsLGv 57 (395)
T PLN03114 20 SDNKICF--DCNAKN-PTWASVTYG-IFLCIDCSAVHRSLGV 57 (395)
T ss_pred cCCCcCc--cCCCCC-CCceeeccc-eeehhhhhHhhccCCC
Confidence 4567898 999875 999999999 9999999777666554
No 31
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor 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. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=22.45 E-value=88 Score=21.84 Aligned_cols=33 Identities=21% Similarity=0.528 Sum_probs=24.2
Q ss_pred CccccCCCCCCCCCCccccCCCCCcchhhHHHHHHHhhhc
Q 047722 78 YKRCTNYNCNTNDTPMWRRGPLGPKTLCNACGIKYRKEEE 117 (138)
Q Consensus 78 ~~~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL~~~k~~~ 117 (138)
...|. -|+...+-.+ .| ...|+||..||++...
T Consensus 6 ~~~C~--VCg~~~~g~h----yG-v~sC~aCk~FFRR~v~ 38 (90)
T cd07168 6 PKLCS--ICEDKATGLH----YG-IITCEGCKGFFKRTVQ 38 (90)
T ss_pred CCCCc--ccCCcCcceE----EC-ceehhhhhHhhhhhhc
Confidence 44588 8886554332 44 6889999999999875
No 32
>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=22.22 E-value=37 Score=20.46 Aligned_cols=34 Identities=26% Similarity=0.629 Sum_probs=20.5
Q ss_pred ccccCCCCCCCCCCc--cccCCCCCcchhhHHHHHHHhh
Q 047722 79 KRCTNYNCNTNDTPM--WRRGPLGPKTLCNACGIKYRKE 115 (138)
Q Consensus 79 ~~C~~~~C~t~~TP~--WRrGp~G~~~LCNACGL~~~k~ 115 (138)
+.|+ .|+...+.. .=.|+.+ ...|+.|-......
T Consensus 2 ~~CS--FCgr~~~~v~~li~g~~~-~~IC~~Cv~~~~~i 37 (41)
T PF06689_consen 2 KRCS--FCGRPESEVGRLISGPNG-AYICDECVEQAYEI 37 (41)
T ss_dssp -B-T--TT--BTTTSSSEEEES-S-EEEEHHHHHHHHHH
T ss_pred CCcc--CCCCCHHHHhceecCCCC-cEECHHHHHHHHHH
Confidence 4699 899887633 2368877 89999997665443
No 33
>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=21.19 E-value=1.6e+02 Score=20.00 Aligned_cols=43 Identities=16% Similarity=0.432 Sum_probs=31.4
Q ss_pred CCccccCCCCCCCCCCcc---ccCCCCCcchhhHHHHHHHhhhcccch
Q 047722 77 PYKRCTNYNCNTNDTPMW---RRGPLGPKTLCNACGIKYRKEEEKRKA 121 (138)
Q Consensus 77 ~~~~C~~~~C~t~~TP~W---RrGp~G~~~LCNACGL~~~k~~~~r~~ 121 (138)
+...|- .|.+++|-.= --...-|...|-+|-.+|-..+..|..
T Consensus 4 ~~~~CP--RC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnV 49 (63)
T PF02701_consen 4 QPLPCP--RCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNV 49 (63)
T ss_pred cCCCCC--CcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCC
Confidence 445687 8888887542 223345789999999999999886654
No 34
>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=20.59 E-value=36 Score=20.31 Aligned_cols=31 Identities=29% Similarity=0.607 Sum_probs=19.9
Q ss_pred CccccCCCCCCCCCCccccCCCCCcchhhHHHH
Q 047722 78 YKRCTNYNCNTNDTPMWRRGPLGPKTLCNACGI 110 (138)
Q Consensus 78 ~~~C~~~~C~t~~TP~WRrGp~G~~~LCNACGL 110 (138)
+-+|. +|++---|.-.-...|..-.||-|+.
T Consensus 2 p~rC~--~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCR--RCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-T--TT--BS-TTSEEETTTTEEEETTT--
T ss_pred ccccC--CCCCEECCcceEcCCCCEEECcCCCC
Confidence 34698 99999988888777877789999985
No 35
>PF15396 FAM60A: Protein Family FAM60A
Probab=20.28 E-value=62 Score=26.73 Aligned_cols=18 Identities=22% Similarity=0.536 Sum_probs=14.2
Q ss_pred CcchhhHHHHHHHhhhcc
Q 047722 101 PKTLCNACGIKYRKEEEK 118 (138)
Q Consensus 101 ~~~LCNACGL~~~k~~~~ 118 (138)
...+||||=|..++-.+.
T Consensus 48 sGeICNACVLLVKRwKKL 65 (213)
T PF15396_consen 48 SGEICNACVLLVKRWKKL 65 (213)
T ss_pred cchhhHHHHHHHHHHhhC
Confidence 358999999998876554
No 36
>PF06869 DUF1258: Protein of unknown function (DUF1258); InterPro: IPR009667 This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to Caenorhabditis elegans. Note that this family contains a number of conserved cysteine and histidine residues.
Probab=20.20 E-value=43 Score=28.36 Aligned_cols=17 Identities=24% Similarity=0.770 Sum_probs=13.1
Q ss_pred ccCCCCCcchhhHHHHH
Q 047722 95 RRGPLGPKTLCNACGIK 111 (138)
Q Consensus 95 RrGp~G~~~LCNACGL~ 111 (138)
+++-.-...+||.||..
T Consensus 11 ~~~~~S~h~~CN~CG~~ 27 (258)
T PF06869_consen 11 KKNNFSTHFICNSCGKV 27 (258)
T ss_pred ccCcceeehhhhhhhhh
Confidence 55556668999999983
Done!