Query 023560
Match_columns 280
No_of_seqs 264 out of 1016
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 04:58:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023560.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023560hhsearch_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 99.6 1.2E-15 2.5E-20 110.4 3.5 44 201-246 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.5 7.2E-15 1.6E-19 105.4 3.3 46 199-246 3-49 (52)
3 PF06200 tify: tify domain; I 99.5 5.4E-14 1.2E-18 93.9 4.9 34 72-105 2-35 (36)
4 PF00320 GATA: GATA zinc finge 99.4 1.6E-14 3.6E-19 96.2 1.0 36 202-239 1-36 (36)
5 PF06203 CCT: CCT motif; Inte 99.4 1.5E-13 3.3E-18 95.9 2.9 44 126-169 1-44 (45)
6 KOG1601 GATA-4/5/6 transcripti 98.7 1.6E-08 3.4E-13 88.6 3.4 52 199-252 199-250 (340)
7 COG5641 GAT1 GATA Zn-finger-co 98.3 2.5E-07 5.4E-12 92.8 1.3 50 198-250 157-212 (498)
8 PF09425 CCT_2: Divergent CCT 98.1 1.3E-06 2.7E-11 55.0 1.6 26 123-149 1-26 (27)
9 COG5641 GAT1 GATA Zn-finger-co 92.6 0.061 1.3E-06 54.7 1.8 51 195-246 293-343 (498)
10 KOG3554 Histone deacetylase co 86.6 2.2 4.7E-05 43.6 7.1 37 199-237 386-424 (693)
11 KOG1601 GATA-4/5/6 transcripti 79.8 0.5 1.1E-05 41.2 -0.4 41 123-163 290-330 (340)
12 PF14803 Nudix_N_2: Nudix N-te 72.2 1.1 2.3E-05 29.7 -0.3 27 200-231 1-30 (34)
13 PF06677 Auto_anti-p27: Sjogre 59.7 4 8.6E-05 28.1 0.6 25 199-230 17-41 (41)
14 PF13619 KTSC: KTSC domain 52.3 27 0.00058 25.2 4.0 31 72-102 12-43 (60)
15 PF01783 Ribosomal_L32p: Ribos 49.2 5.7 0.00012 28.7 0.0 28 198-237 25-52 (56)
16 COG3952 Predicted membrane pro 48.7 4 8.7E-05 33.8 -0.9 21 213-235 75-95 (113)
17 KOG3740 Uncharacterized conser 48.6 6.5 0.00014 41.4 0.3 35 199-235 462-499 (706)
18 COG1645 Uncharacterized Zn-fin 45.3 8.2 0.00018 33.0 0.4 26 198-231 27-52 (131)
19 PF02701 zf-Dof: Dof domain, z 45.0 13 0.00028 28.0 1.3 47 198-246 4-53 (63)
20 PRK03988 translation initiatio 44.9 7.3 0.00016 33.3 0.0 31 198-231 101-131 (138)
21 PF13717 zinc_ribbon_4: zinc-r 44.6 5 0.00011 26.5 -0.8 33 200-233 3-35 (36)
22 PRK00420 hypothetical protein; 43.5 10 0.00023 31.5 0.7 30 199-235 23-52 (112)
23 TIGR00311 aIF-2beta translatio 42.2 8.7 0.00019 32.7 0.1 31 198-231 96-126 (133)
24 PRK11823 DNA repair protein Ra 41.7 10 0.00023 37.9 0.6 27 198-234 6-32 (446)
25 PRK12336 translation initiatio 41.0 16 0.00034 32.9 1.6 31 198-231 97-127 (201)
26 smart00653 eIF2B_5 domain pres 40.3 10 0.00022 31.3 0.2 30 199-231 80-109 (110)
27 PF01412 ArfGap: Putative GTPa 40.1 24 0.00052 28.7 2.4 38 197-238 11-48 (116)
28 PF06689 zf-C4_ClpX: ClpX C4-t 39.0 15 0.00033 24.9 0.9 32 200-232 2-33 (41)
29 PRK05978 hypothetical protein; 38.2 14 0.0003 32.1 0.8 33 199-236 33-65 (148)
30 TIGR00416 sms DNA repair prote 37.2 14 0.00031 37.1 0.8 25 198-232 6-30 (454)
31 COG5349 Uncharacterized protei 36.9 13 0.00028 31.5 0.3 34 199-237 21-54 (126)
32 PF08271 TF_Zn_Ribbon: TFIIB z 35.1 14 0.00031 24.9 0.3 29 201-234 2-30 (43)
33 cd01121 Sms Sms (bacterial rad 34.7 16 0.00034 35.9 0.6 23 201-233 2-24 (372)
34 COG2331 Uncharacterized protei 33.6 14 0.00029 29.1 -0.1 35 199-236 12-46 (82)
35 PF01873 eIF-5_eIF-2B: Domain 32.6 17 0.00038 30.5 0.4 29 200-231 94-122 (125)
36 COG4260 Membrane protease subu 31.1 27 0.00057 33.9 1.4 29 198-231 314-342 (345)
37 COG2816 NPY1 NTP pyrophosphohy 29.7 20 0.00043 34.3 0.3 32 198-235 110-141 (279)
38 PRK05342 clpX ATP-dependent pr 29.6 34 0.00073 34.1 2.0 30 199-230 9-38 (412)
39 PRK14892 putative transcriptio 29.6 19 0.00041 29.3 0.1 36 198-236 20-55 (99)
40 PF13248 zf-ribbon_3: zinc-rib 29.0 34 0.00073 20.8 1.2 22 200-231 3-24 (26)
41 PRK12496 hypothetical protein; 28.6 30 0.00066 30.1 1.3 34 200-241 128-161 (164)
42 PRK12286 rpmF 50S ribosomal pr 28.4 22 0.00048 26.0 0.4 24 198-232 26-49 (57)
43 PF09297 zf-NADH-PPase: NADH p 28.4 11 0.00024 24.0 -1.2 28 199-232 3-30 (32)
44 TIGR02098 MJ0042_CXXC MJ0042 f 28.0 11 0.00024 24.5 -1.2 33 200-233 3-35 (38)
45 PF04810 zf-Sec23_Sec24: Sec23 27.9 23 0.0005 23.7 0.3 31 199-231 2-32 (40)
46 smart00834 CxxC_CXXC_SSSS Puta 27.4 29 0.00062 22.5 0.7 29 200-231 6-34 (41)
47 PF09889 DUF2116: Uncharacteri 26.8 29 0.00062 25.7 0.7 29 199-237 3-32 (59)
48 TIGR03573 WbuX N-acetyl sugar 26.8 51 0.0011 31.7 2.6 32 200-235 2-33 (343)
49 smart00105 ArfGap Putative GTP 25.3 58 0.0012 26.4 2.3 44 198-245 2-49 (112)
50 KOG1598 Transcription initiati 24.2 35 0.00077 35.3 1.0 32 201-237 2-33 (521)
51 PF13240 zinc_ribbon_2: zinc-r 22.6 50 0.0011 19.8 1.1 8 224-231 14-21 (23)
52 PF09723 Zn-ribbon_8: Zinc rib 22.6 39 0.00084 22.8 0.6 29 200-231 6-34 (42)
53 TIGR03655 anti_R_Lar restricti 22.0 38 0.00083 23.9 0.6 29 199-231 1-34 (53)
54 PF14122 YokU: YokU-like prote 21.9 33 0.00071 27.4 0.2 16 223-238 35-50 (87)
55 PF15396 FAM60A: Protein Famil 21.7 47 0.001 30.6 1.2 21 224-244 50-70 (213)
56 PF12773 DZR: Double zinc ribb 21.1 59 0.0013 22.1 1.3 28 198-232 11-38 (50)
57 TIGR02605 CxxC_CxxC_SSSS putat 20.9 46 0.00099 22.9 0.8 29 200-231 6-34 (52)
58 COG3529 Predicted nucleic-acid 20.6 21 0.00046 26.9 -1.0 32 200-234 11-43 (66)
59 smart00661 RPOL9 RNA polymeras 20.6 43 0.00094 22.8 0.6 29 201-234 2-31 (52)
60 PF09692 Arb1: Argonaute siRNA 20.4 68 0.0015 32.1 2.1 15 124-138 46-61 (396)
61 COG1066 Sms Predicted ATP-depe 20.0 40 0.00087 34.3 0.4 25 198-232 6-30 (456)
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=99.57 E-value=1.2e-15 Score=110.36 Aligned_cols=44 Identities=55% Similarity=1.175 Sum_probs=41.5
Q ss_pred cccccccccCCCCceecCCCCCCccchhhhHhHHhcCCCCCCCcCC
Q 023560 201 VCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGTLRDLSKAA 246 (280)
Q Consensus 201 ~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~~g~~r~~~~~~ 246 (280)
.|+||++ +.||+||+||.+..+|||||||||++++..||+.+..
T Consensus 1 ~C~~C~~--~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGT--TTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRK 44 (54)
T ss_pred CCCCCCC--CCCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCc
Confidence 4999999 7999999999888999999999999999999999876
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.51 E-value=7.2e-15 Score=105.36 Aligned_cols=46 Identities=50% Similarity=1.007 Sum_probs=41.6
Q ss_pred cccccccccccCCCCceecCCCCCCccchhhhHhHHhcCCC-CCCCcCC
Q 023560 199 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGTL-RDLSKAA 246 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~~g~~-r~~~~~~ 246 (280)
...|++|++ +.||+||+||.|.++|||||||||++++.+ ||+.+..
T Consensus 3 ~~~C~~C~~--~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~~ 49 (52)
T smart00401 3 GRSCSNCGT--TETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLKK 49 (52)
T ss_pred CCCcCCCCC--CCCCccccCCCCCCcEeecccHHHHHcCCCCCcccccc
Confidence 467999999 789999999999889999999999999998 8877654
No 3
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=99.48 E-value=5.4e-14 Score=93.95 Aligned_cols=34 Identities=47% Similarity=0.705 Sum_probs=31.9
Q ss_pred CCCCCceEEEeccEEeeecCCCHHHHHHHHHHhC
Q 023560 72 SEIGDQLTLSFQGQVYVFDSVSPEKVQAVLLLLG 105 (280)
Q Consensus 72 ~~~~aqLTify~G~v~Vfd~v~p~Kaq~im~la~ 105 (280)
.+.++||||||+|+|+|||+||++||++||+||+
T Consensus 2 ~~~~~qLTIfY~G~V~Vfd~v~~~Ka~~im~lA~ 35 (36)
T PF06200_consen 2 SPETAQLTIFYGGQVCVFDDVPPDKAQEIMLLAS 35 (36)
T ss_pred CCCCCcEEEEECCEEEEeCCCCHHHHHHHHHHhc
Confidence 3578999999999999999999999999999996
No 4
>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=1.6e-14 Score=96.18 Aligned_cols=36 Identities=56% Similarity=1.214 Sum_probs=28.4
Q ss_pred ccccccccCCCCceecCCCCCCccchhhhHhHHhcCCC
Q 023560 202 CRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGTL 239 (280)
Q Consensus 202 C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~~g~~ 239 (280)
|++|++ +.||+||++|.|..+|||||||+|++++++
T Consensus 1 C~~C~t--t~t~~WR~~~~g~~~LCn~Cg~~~kk~~~~ 36 (36)
T PF00320_consen 1 CSNCGT--TETPQWRRGPNGNRTLCNACGLYYKKYGKM 36 (36)
T ss_dssp -TTT----ST-SSEEEETTSEE-EEHHHHHHHHHHSS-
T ss_pred CcCCcC--CCCchhhcCCCCCCHHHHHHHHHHHHhCCC
Confidence 899999 789999999999888999999999999864
No 5
>PF06203 CCT: CCT motif; InterPro: IPR010402 The CCT (CONSTANS, CO-like, and TOC1) domain is a highly conserved basic module of ~43 amino acids, which is found near the C terminus of plant proteins often involved in light signal transduction. The CCT domain is found in association with other domains, such as the B-box zinc finger, the GATA-type zinc finger, the ZIM motif or the response regulatory domain. The CCT domain contains a putative nuclear localisation signal within the second half of the CCT motif and has been shown to be involved in nuclear localization and probably also has a role in protein-protein interaction [].; GO: 0005515 protein binding
Probab=99.39 E-value=1.5e-13 Score=95.93 Aligned_cols=44 Identities=57% Similarity=0.801 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHhhhhcccccccchhhHHHHHHHhhccccccccc
Q 023560 126 RLASLIRFREKRKERNFEKKIRYTVRKEVALRMQRNKGQFTSAK 169 (280)
Q Consensus 126 R~asl~r~~eKrk~r~f~kkirY~~RK~~A~~rpR~KGrf~s~k 169 (280)
|.++|+||++||+.|+|.|+|+|++||.+|+.|||+||+|++..
T Consensus 1 R~~~l~Ry~~Kr~~R~f~kkirY~~Rk~~A~~R~RvkGRFvk~~ 44 (45)
T PF06203_consen 1 REEKLQRYREKRKRRNFEKKIRYESRKAVADKRPRVKGRFVKKS 44 (45)
T ss_pred CHHHHHHHHHHHHhhcccccCCcchHHHHHhhCCccCCcccCCC
Confidence 67899999999999999999999999999999999999999864
No 6
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.65 E-value=1.6e-08 Score=88.58 Aligned_cols=52 Identities=44% Similarity=0.940 Sum_probs=45.0
Q ss_pred cccccccccccCCCCceecCCCCCCccchhhhHhHHhcCCCCCCCcCCCCCCCC
Q 023560 199 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGTLRDLSKAAPQAGQT 252 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~~g~~r~~~~~~~~~~~~ 252 (280)
...|.+|++ +.||+||++|.|++++|||||++|++++..|++.++.......
T Consensus 199 ~~~c~~~~~--~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~ 250 (340)
T KOG1601|consen 199 LRQCSNCGT--TKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPR 250 (340)
T ss_pred CcccCCCCC--CCCcceecCCCCCccccccchhhhhhcCccccccccCcccccc
Confidence 579999999 7999999999999999999999999998778877777654433
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.27 E-value=2.5e-07 Score=92.83 Aligned_cols=50 Identities=40% Similarity=0.725 Sum_probs=43.3
Q ss_pred ccccccccccccCCCCceecCCC-----CCCccchhhhHhHHhcCCCC-CCCcCCCCCC
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPE-----GPRTLCNACGLMWANKGTLR-DLSKAAPQAG 250 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~-----G~~~LCNACGl~~~~~g~~r-~~~~~~~~~~ 250 (280)
...+|.||.+ +.||+|||+.. | -.|||||||+|+.||++| |+..+.-..-
T Consensus 157 ~~~vc~Nc~t--~stPlwrR~~~~~s~~~-n~lcnaCgl~~klhg~~r~P~t~ks~~~k 212 (498)
T COG5641 157 QPHVCSNCKT--TSTPLWRRASSESSLPG-NNLCNACGLYLKLHGSPRAPISLKSDSIK 212 (498)
T ss_pred ccchhccccc--cCCccccccccccccCC-ccccccccccccccCCcCCCccccccccc
Confidence 3349999999 78999999999 6 599999999999999999 8888765443
No 8
>PF09425 CCT_2: Divergent CCT motif; InterPro: IPR018467 The short CCT (CO, COL, TOC1) motif is found in a number of plant proteins, including Constans (CO), Constans-like (COL) and TOC1. The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif []. The CCT motif is found in the Arabidopsis circadian rhythm protein TOC1, an autoregulatory response regulator homologue the controls the photoperiodic flowering through its clock function []. ; GO: 0005515 protein binding; PDB: 3OGK_V 3OGL_S 3OGM_W.
Probab=98.12 E-value=1.3e-06 Score=54.99 Aligned_cols=26 Identities=50% Similarity=0.508 Sum_probs=10.0
Q ss_pred hHHHHHHHHHHHHHhhhhcccccccch
Q 023560 123 NNRRLASLIRFREKRKERNFEKKIRYT 149 (280)
Q Consensus 123 ~~~R~asl~r~~eKrk~r~f~kkirY~ 149 (280)
|++|++||+||+||||+|+.. +..|.
T Consensus 1 P~aRK~SLqRFLeKRK~R~~~-~~PY~ 26 (27)
T PF09425_consen 1 PIARKASLQRFLEKRKDRLAA-KSPYQ 26 (27)
T ss_dssp -----HHHHHHHHHH------------
T ss_pred CchHHHHHHHHHHHHHHhhcc-CCCCC
Confidence 578999999999999999988 55564
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=92.64 E-value=0.061 Score=54.71 Aligned_cols=51 Identities=25% Similarity=0.285 Sum_probs=43.7
Q ss_pred CccccccccccccccCCCCceecCCCCCCccchhhhHhHHhcCCCCCCCcCC
Q 023560 195 SQNQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGTLRDLSKAA 246 (280)
Q Consensus 195 ~~~~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~~g~~r~~~~~~ 246 (280)
..+....|.+|.+. +.||.||+...-.-.+|||||++.+..+..||+..+.
T Consensus 293 ~~ps~~~~s~~~~~-~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~ 343 (498)
T COG5641 293 VLPSDKKRSTLTTS-TATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKP 343 (498)
T ss_pred cchhhcCccccccc-ccCcccccccccccccccccccccCCcccccccCCCC
Confidence 34557889999987 6899999988776799999999999999999998854
No 10
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=86.57 E-value=2.2 Score=43.55 Aligned_cols=37 Identities=24% Similarity=0.599 Sum_probs=29.2
Q ss_pred cccccccccccCCCCceec-CC-CCCCccchhhhHhHHhcC
Q 023560 199 DIVCRHCGISEKSTPMMRR-GP-EGPRTLCNACGLMWANKG 237 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~wR~-Gp-~G~~~LCNACGl~~~~~g 237 (280)
.+.|.+|++ ++.-.|=. || .-...||--|=+||+|.|
T Consensus 386 g~~CEsC~t--tqs~qWYsWGppnmqcrLCasCWiyWKKyg 424 (693)
T KOG3554|consen 386 GRACESCYT--TQSLQWYSWGPPNMQCRLCASCWIYWKKYG 424 (693)
T ss_pred CCccccccc--ccccceeccCCCCccchhhHHHHHHHHHhc
Confidence 678999999 67777754 44 444479999999999986
No 11
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=79.79 E-value=0.5 Score=41.25 Aligned_cols=41 Identities=44% Similarity=0.657 Sum_probs=38.4
Q ss_pred hHHHHHHHHHHHHHhhhhcccccccchhhHHHHHHHhhccc
Q 023560 123 NNRRLASLIRFREKRKERNFEKKIRYTVRKEVALRMQRNKG 163 (280)
Q Consensus 123 ~~~R~asl~r~~eKrk~r~f~kkirY~~RK~~A~~rpR~KG 163 (280)
...|.+.+.||+++++.+.|.++++|..++..+..+++.++
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 45788999999999999999999999999999999999988
No 12
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=72.24 E-value=1.1 Score=29.69 Aligned_cols=27 Identities=41% Similarity=1.015 Sum_probs=14.1
Q ss_pred ccccccccccCCCCcee---cCCCCCCccchhhhH
Q 023560 200 IVCRHCGISEKSTPMMR---RGPEGPRTLCNACGL 231 (280)
Q Consensus 200 ~~C~~Cg~~~~~Tp~wR---~Gp~G~~~LCNACGl 231 (280)
+.|.+||. |+=+ .|.+-.+..|.+||-
T Consensus 1 kfC~~CG~-----~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGG-----PLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT-------B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccC-----hhhhhcCCCCCccceECCCCCC
Confidence 36999998 3333 345555679999984
No 13
>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=59.66 E-value=4 Score=28.07 Aligned_cols=25 Identities=44% Similarity=1.163 Sum_probs=19.1
Q ss_pred cccccccccccCCCCceecCCCCCCccchhhh
Q 023560 199 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACG 230 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACG 230 (280)
...|..|++ |++| ..+| +.+|-+|+
T Consensus 17 ~~~Cp~C~~-----PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGT-----PLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred cCccCCCCC-----eeEE-ecCC-CEECCCCC
Confidence 356999965 9999 3466 68999885
No 14
>PF13619 KTSC: KTSC domain
Probab=52.31 E-value=27 Score=25.21 Aligned_cols=31 Identities=32% Similarity=0.486 Sum_probs=26.1
Q ss_pred CCCCCceEEEe-ccEEeeecCCCHHHHHHHHH
Q 023560 72 SEIGDQLTLSF-QGQVYVFDSVSPEKVQAVLL 102 (280)
Q Consensus 72 ~~~~aqLTify-~G~v~Vfd~v~p~Kaq~im~ 102 (280)
...+..|.|.| .|.++.|.+||+.-.+++|.
T Consensus 12 d~~~~~L~V~F~~G~~Y~Y~~Vp~~~~~~l~~ 43 (60)
T PF13619_consen 12 DPETRTLEVEFKSGSVYRYFGVPPEVYEALLN 43 (60)
T ss_pred CCCCCEEEEEEcCCCEEEECCCCHHHHHHHHc
Confidence 35577899888 89999999999999988754
No 15
>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=49.19 E-value=5.7 Score=28.72 Aligned_cols=28 Identities=25% Similarity=0.793 Sum_probs=19.1
Q ss_pred ccccccccccccCCCCceecCCCCCCccchhhhHhHHhcC
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKG 237 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~~g 237 (280)
....|.+||.. . -+..+|..|| ||+.+.
T Consensus 25 ~l~~c~~cg~~--~---------~~H~vc~~cG-~y~~r~ 52 (56)
T PF01783_consen 25 NLVKCPNCGEP--K---------LPHRVCPSCG-YYKGRQ 52 (56)
T ss_dssp SEEESSSSSSE--E---------STTSBCTTTB-BSSSSS
T ss_pred ceeeeccCCCE--e---------cccEeeCCCC-eECCEE
Confidence 45779999972 1 1258999999 555443
No 16
>COG3952 Predicted membrane protein [Function unknown]
Probab=48.68 E-value=4 Score=33.79 Aligned_cols=21 Identities=33% Similarity=0.408 Sum_probs=16.4
Q ss_pred CceecCCCCCCccchhhhHhHHh
Q 023560 213 PMMRRGPEGPRTLCNACGLMWAN 235 (280)
Q Consensus 213 p~wR~Gp~G~~~LCNACGl~~~~ 235 (280)
-+||.+|-+ .||++|||+-..
T Consensus 75 fi~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 75 FIRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHHhcchHH--HHHHhhhHHHHH
Confidence 357788887 799999997543
No 17
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=48.60 E-value=6.5 Score=41.38 Aligned_cols=35 Identities=17% Similarity=0.433 Sum_probs=28.0
Q ss_pred cccccccccccCCCCceecCCCC---CCccchhhhHhHHh
Q 023560 199 DIVCRHCGISEKSTPMMRRGPEG---PRTLCNACGLMWAN 235 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~wR~Gp~G---~~~LCNACGl~~~~ 235 (280)
...|..|.+ .-||.|+.-+.+ ..++|.+|----.|
T Consensus 462 P~~caqckt--dftp~wk~ekstq~d~~i~cE~cvtSnqk 499 (706)
T KOG3740|consen 462 PYACAQCKT--DFTPAWKKEKSTQADAAIVCENCVTSNQK 499 (706)
T ss_pred chhhhhccc--ccccccccccccCcchHHHHHhhhhhccc
Confidence 578999999 789999998777 34799999764333
No 18
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=45.28 E-value=8.2 Score=32.98 Aligned_cols=26 Identities=35% Similarity=1.016 Sum_probs=22.0
Q ss_pred ccccccccccccCCCCceecCCCCCCccchhhhH
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 231 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl 231 (280)
....|.-||+ |++| -+| ..+|--||.
T Consensus 27 L~~hCp~Cg~-----PLF~--KdG-~v~CPvC~~ 52 (131)
T COG1645 27 LAKHCPKCGT-----PLFR--KDG-EVFCPVCGY 52 (131)
T ss_pred HHhhCcccCC-----ccee--eCC-eEECCCCCc
Confidence 3467999997 9999 588 699999994
No 19
>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=45.04 E-value=13 Score=28.03 Aligned_cols=47 Identities=28% Similarity=0.680 Sum_probs=32.4
Q ss_pred ccccccccccccCCCCce--ec-CCCCCCccchhhhHhHHhcCCCCCCCcCC
Q 023560 198 QDIVCRHCGISEKSTPMM--RR-GPEGPRTLCNACGLMWANKGTLRDLSKAA 246 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~w--R~-Gp~G~~~LCNACGl~~~~~g~~r~~~~~~ 246 (280)
....|..|.. +.|-.- =. ...-|+.+|-+|-.+|-..|.+|.++-+.
T Consensus 4 ~~~~CPRC~S--~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvgg 53 (63)
T PF02701_consen 4 QPLPCPRCDS--TNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGG 53 (63)
T ss_pred cCCCCCCcCC--CCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCC
Confidence 4577888886 344220 00 12345689999999999999999986543
No 20
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=44.94 E-value=7.3 Score=33.35 Aligned_cols=31 Identities=29% Similarity=0.730 Sum_probs=22.3
Q ss_pred ccccccccccccCCCCceecCCCCCCccchhhhH
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 231 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl 231 (280)
.-..|..|+. ..|-+-+++-.= -.-|+|||-
T Consensus 101 ~yVlC~~C~s--pdT~l~k~~r~~-~l~C~ACGa 131 (138)
T PRK03988 101 EYVICPECGS--PDTKLIKEGRIW-VLKCEACGA 131 (138)
T ss_pred hcEECCCCCC--CCcEEEEcCCeE-EEEcccCCC
Confidence 3468999999 478887753221 358999996
No 21
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=44.56 E-value=5 Score=26.54 Aligned_cols=33 Identities=24% Similarity=0.652 Sum_probs=26.5
Q ss_pred ccccccccccCCCCceecCCCCCCccchhhhHhH
Q 023560 200 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMW 233 (280)
Q Consensus 200 ~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~ 233 (280)
..|.+|++. ...+..+-.+.|...-|-.||-.|
T Consensus 3 i~Cp~C~~~-y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAK-YEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCE-EeCCHHHCCCCCcEEECCCCCCEe
Confidence 469999986 567777778888888999998755
No 22
>PRK00420 hypothetical protein; Validated
Probab=43.45 E-value=10 Score=31.47 Aligned_cols=30 Identities=23% Similarity=0.707 Sum_probs=23.5
Q ss_pred cccccccccccCCCCceecCCCCCCccchhhhHhHHh
Q 023560 199 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWAN 235 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~ 235 (280)
...|..||+ |+.|- ..| +.+|-.||-.+..
T Consensus 23 ~~~CP~Cg~-----pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCGL-----PLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCCC-----cceec-CCC-ceECCCCCCeeee
Confidence 357999987 88885 466 6999999986554
No 23
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=42.24 E-value=8.7 Score=32.69 Aligned_cols=31 Identities=29% Similarity=0.762 Sum_probs=21.8
Q ss_pred ccccccccccccCCCCceecCCCCCCccchhhhH
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 231 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl 231 (280)
.-..|..|+- ..|-+-+.+--- -.-|+|||-
T Consensus 96 ~yVlC~~C~s--PdT~l~k~~r~~-~l~C~ACGa 126 (133)
T TIGR00311 96 KYVICRECNR--PDTRIIKEGRVS-LLKCEACGA 126 (133)
T ss_pred heEECCCCCC--CCcEEEEeCCeE-EEecccCCC
Confidence 3467999999 468887753211 247999996
No 24
>PRK11823 DNA repair protein RadA; Provisional
Probab=41.72 E-value=10 Score=37.87 Aligned_cols=27 Identities=33% Similarity=0.811 Sum_probs=17.9
Q ss_pred ccccccccccccCCCCceecCCCCCCccchhhhHhHH
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWA 234 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~ 234 (280)
...+|.+||.. ++.|- | -|.+||-|=-
T Consensus 6 ~~y~C~~Cg~~---~~~~~----g---~Cp~C~~w~t 32 (446)
T PRK11823 6 TAYVCQECGAE---SPKWL----G---RCPECGAWNT 32 (446)
T ss_pred CeEECCcCCCC---CcccC----e---eCcCCCCccc
Confidence 45789999984 55552 2 5888876533
No 25
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=41.04 E-value=16 Score=32.94 Aligned_cols=31 Identities=26% Similarity=0.725 Sum_probs=22.3
Q ss_pred ccccccccccccCCCCceecCCCCCCccchhhhH
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 231 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl 231 (280)
.-..|..|+- ..|-+-+.+..= -.-|+|||-
T Consensus 97 ~yV~C~~C~~--pdT~l~k~~~~~-~l~C~aCGa 127 (201)
T PRK12336 97 EYVICSECGL--PDTRLVKEDRVL-MLRCDACGA 127 (201)
T ss_pred heEECCCCCC--CCcEEEEcCCeE-EEEcccCCC
Confidence 3468999999 578887764211 247999997
No 26
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=40.34 E-value=10 Score=31.29 Aligned_cols=30 Identities=27% Similarity=0.626 Sum_probs=21.3
Q ss_pred cccccccccccCCCCceecCCCCCCccchhhhH
Q 023560 199 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 231 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl 231 (280)
-..|..|+. .+|-+-+.+-.= -.-|+|||-
T Consensus 80 yVlC~~C~s--pdT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 80 YVLCPECGS--PDTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred cEECCCCCC--CCcEEEEeCCeE-EEEccccCC
Confidence 367999999 478888773211 245999994
No 27
>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=40.10 E-value=24 Score=28.73 Aligned_cols=38 Identities=26% Similarity=0.500 Sum_probs=27.0
Q ss_pred cccccccccccccCCCCceecCCCCCCccchhhhHhHHhcCC
Q 023560 197 NQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGT 238 (280)
Q Consensus 197 ~~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~~g~ 238 (280)
+....|..|+. .-|.|-.=.-| -.||-.|.-..+.-|+
T Consensus 11 ~~N~~CaDCg~---~~p~w~s~~~G-iflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 11 PGNKVCADCGA---PNPTWASLNYG-IFLCLECAGIHRSLGV 48 (116)
T ss_dssp TTCTB-TTT-S---BS--EEETTTT-EEE-HHHHHHHHHHTT
T ss_pred cCcCcCCCCCC---CCCCEEEeecC-hhhhHHHHHHHHHhcc
Confidence 45688999998 46899998888 6999999988877764
No 28
>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=38.96 E-value=15 Score=24.89 Aligned_cols=32 Identities=28% Similarity=0.668 Sum_probs=20.2
Q ss_pred ccccccccccCCCCceecCCCCCCccchhhhHh
Q 023560 200 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 232 (280)
Q Consensus 200 ~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~ 232 (280)
..|+-||.+....-..=.||.+ .-.|+.|-..
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~-~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNG-AYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-S-EEEEHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCC-cEECHHHHHH
Confidence 5799999976655555578877 5899999754
No 29
>PRK05978 hypothetical protein; Provisional
Probab=38.22 E-value=14 Score=32.10 Aligned_cols=33 Identities=27% Similarity=0.548 Sum_probs=24.9
Q ss_pred cccccccccccCCCCceecCCCCCCccchhhhHhHHhc
Q 023560 199 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANK 236 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~~ 236 (280)
..+|.+||. ..++| +--.-..-|.+||+.|..+
T Consensus 33 ~grCP~CG~----G~LF~-g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 33 RGRCPACGE----GKLFR-AFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred cCcCCCCCC----Ccccc-cccccCCCccccCCccccC
Confidence 458999997 46776 4455568999999977654
No 30
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=37.24 E-value=14 Score=37.06 Aligned_cols=25 Identities=32% Similarity=0.691 Sum_probs=16.5
Q ss_pred ccccccccccccCCCCceecCCCCCCccchhhhHh
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 232 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~ 232 (280)
...+|.+||.. ...|+| -|.+|+-|
T Consensus 6 ~~y~C~~Cg~~-~~~~~g---------~Cp~C~~w 30 (454)
T TIGR00416 6 SKFVCQHCGAD-SPKWQG---------KCPACHAW 30 (454)
T ss_pred CeEECCcCCCC-CccccE---------ECcCCCCc
Confidence 34789999984 234444 48888764
No 31
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.91 E-value=13 Score=31.52 Aligned_cols=34 Identities=29% Similarity=0.550 Sum_probs=23.0
Q ss_pred cccccccccccCCCCceecCCCCCCccchhhhHhHHhcC
Q 023560 199 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKG 237 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~~g 237 (280)
.-+|.+||- -=+.| |=-...+-|.|||+-|-.+.
T Consensus 21 ~grCP~CGe----GrLF~-gFLK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 21 RGRCPRCGE----GRLFR-GFLKVVPACEACGLDYGFAD 54 (126)
T ss_pred cCCCCCCCC----chhhh-hhcccCchhhhccccccCCc
Confidence 457999997 23333 33444579999999776553
No 32
>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=35.14 E-value=14 Score=24.86 Aligned_cols=29 Identities=28% Similarity=0.763 Sum_probs=16.4
Q ss_pred cccccccccCCCCceecCCCCCCccchhhhHhHH
Q 023560 201 VCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWA 234 (280)
Q Consensus 201 ~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~ 234 (280)
.|.+|+.. . .--.--.| ..+|..||+-+.
T Consensus 2 ~Cp~Cg~~--~--~~~D~~~g-~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCPNCGSK--E--IVFDPERG-ELVCPNCGLVLE 30 (43)
T ss_dssp SBTTTSSS--E--EEEETTTT-EEEETTT-BBEE
T ss_pred CCcCCcCC--c--eEEcCCCC-eEECCCCCCEee
Confidence 58888872 2 22222234 578888887443
No 33
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=34.72 E-value=16 Score=35.90 Aligned_cols=23 Identities=39% Similarity=0.895 Sum_probs=15.0
Q ss_pred cccccccccCCCCceecCCCCCCccchhhhHhH
Q 023560 201 VCRHCGISEKSTPMMRRGPEGPRTLCNACGLMW 233 (280)
Q Consensus 201 ~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~ 233 (280)
+|.+||. .+|.|- | -|.+||-|-
T Consensus 2 ~c~~cg~---~~~~~~----g---~cp~c~~w~ 24 (372)
T cd01121 2 VCSECGY---VSPKWL----G---KCPECGEWN 24 (372)
T ss_pred CCCCCCC---CCCCcc----E---ECcCCCCce
Confidence 5889988 355552 2 477887643
No 34
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.58 E-value=14 Score=29.09 Aligned_cols=35 Identities=26% Similarity=0.520 Sum_probs=24.6
Q ss_pred cccccccccccCCCCceecCCCCCCccchhhhHhHHhc
Q 023560 199 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANK 236 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~~ 236 (280)
.-.|.+|+-.-+.-..++..|. +.|.+||-.+++.
T Consensus 12 ~Y~c~~cg~~~dvvq~~~ddpl---t~ce~c~a~~kk~ 46 (82)
T COG2331 12 SYECTECGNRFDVVQAMTDDPL---TTCEECGARLKKL 46 (82)
T ss_pred EEeecccchHHHHHHhcccCcc---ccChhhChHHHHh
Confidence 4579999984333445666654 5899999977774
No 35
>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=32.55 E-value=17 Score=30.49 Aligned_cols=29 Identities=31% Similarity=0.757 Sum_probs=22.2
Q ss_pred ccccccccccCCCCceecCCCCCCccchhhhH
Q 023560 200 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 231 (280)
Q Consensus 200 ~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl 231 (280)
..|..|+. ..|-+-+++..- -.-|+|||-
T Consensus 94 VlC~~C~s--pdT~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGS--PDTELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp SSCTSTSS--SSEEEEEETTCC-EEEETTTSC
T ss_pred EEcCCCCC--CccEEEEcCCEE-EEEecccCC
Confidence 67999998 578888774333 468999994
No 36
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=31.14 E-value=27 Score=33.91 Aligned_cols=29 Identities=28% Similarity=0.599 Sum_probs=21.4
Q ss_pred ccccccccccccCCCCceecCCCCCCccchhhhH
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 231 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl 231 (280)
....|.+||+ ..|+- =++|..-+|-+||.
T Consensus 314 k~nfc~ncG~--~~t~~---~~ng~a~fcp~cgq 342 (345)
T COG4260 314 KLNFCLNCGC--GTTAD---FDNGKAKFCPECGQ 342 (345)
T ss_pred ccccccccCc--ccccC---CccchhhhChhhcC
Confidence 4458999997 46664 35665679999996
No 37
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=29.71 E-value=20 Score=34.29 Aligned_cols=32 Identities=25% Similarity=0.572 Sum_probs=22.3
Q ss_pred ccccccccccccCCCCceecCCCCCCccchhhhHhHHh
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWAN 235 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~ 235 (280)
..+.|..||+. ..+ ...|-+.+|+.||..+-.
T Consensus 110 ~~RFCg~CG~~--~~~----~~~g~~~~C~~cg~~~fP 141 (279)
T COG2816 110 SHRFCGRCGTK--TYP----REGGWARVCPKCGHEHFP 141 (279)
T ss_pred hCcCCCCCCCc--Ccc----ccCceeeeCCCCCCccCC
Confidence 45789999993 333 234556899999986644
No 38
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=29.65 E-value=34 Score=34.09 Aligned_cols=30 Identities=27% Similarity=0.654 Sum_probs=24.3
Q ss_pred cccccccccccCCCCceecCCCCCCccchhhh
Q 023560 199 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACG 230 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACG 230 (280)
...|+.||.+...+...-.||.. ..|+.|-
T Consensus 9 ~~~CSFCGr~~~ev~~li~g~~~--~IC~~Ci 38 (412)
T PRK05342 9 LLYCSFCGKSQHEVRKLIAGPGV--YICDECI 38 (412)
T ss_pred ccccCCCCCChhhccccccCCCC--cccchHH
Confidence 45899999987777777788854 6999994
No 39
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=29.58 E-value=19 Score=29.29 Aligned_cols=36 Identities=22% Similarity=0.424 Sum_probs=22.8
Q ss_pred ccccccccccccCCCCceecCCCCCCccchhhhHhHHhc
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANK 236 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~~ 236 (280)
....|.+|+.. .-+. ..+-..+...|-.||.|+.+.
T Consensus 20 t~f~CP~Cge~--~v~v-~~~k~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 20 KIFECPRCGKV--SISV-KIKKNIAIITCGNCGLYTEFE 55 (99)
T ss_pred cEeECCCCCCe--Eeee-ecCCCcceEECCCCCCccCEE
Confidence 34679999952 2221 122245578999999987663
No 40
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=29.05 E-value=34 Score=20.81 Aligned_cols=22 Identities=27% Similarity=0.874 Sum_probs=14.2
Q ss_pred ccccccccccCCCCceecCCCCCCccchhhhH
Q 023560 200 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 231 (280)
Q Consensus 200 ~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl 231 (280)
+.|.+||.. . +.+ ..+|-.||.
T Consensus 3 ~~Cp~Cg~~--~-------~~~-~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAE--I-------DPD-AKFCPNCGA 24 (26)
T ss_pred CCCcccCCc--C-------Ccc-cccChhhCC
Confidence 568888872 1 222 468888885
No 41
>PRK12496 hypothetical protein; Provisional
Probab=28.64 E-value=30 Score=30.14 Aligned_cols=34 Identities=26% Similarity=0.482 Sum_probs=23.7
Q ss_pred ccccccccccCCCCceecCCCCCCccchhhhHhHHhcCCCCC
Q 023560 200 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGTLRD 241 (280)
Q Consensus 200 ~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~~g~~r~ 241 (280)
.+|.-|+. ..+. .+.+ ..|.-||...+++...+.
T Consensus 128 ~~C~gC~~---~~~~---~~~~--~~C~~CG~~~~r~~~~~~ 161 (164)
T PRK12496 128 KVCKGCKK---KYPE---DYPD--DVCEICGSPVKRKMVKRR 161 (164)
T ss_pred EECCCCCc---cccC---CCCC--CcCCCCCChhhhcchhhh
Confidence 67999997 3333 3333 599999999888765443
No 42
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=28.43 E-value=22 Score=25.97 Aligned_cols=24 Identities=29% Similarity=0.861 Sum_probs=17.3
Q ss_pred ccccccccccccCCCCceecCCCCCCccchhhhHh
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 232 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~ 232 (280)
....|.+||.. .- +..+|..||.|
T Consensus 26 ~l~~C~~CG~~--~~---------~H~vC~~CG~Y 49 (57)
T PRK12286 26 GLVECPNCGEP--KL---------PHRVCPSCGYY 49 (57)
T ss_pred cceECCCCCCc--cC---------CeEECCCCCcC
Confidence 45679999983 22 25899999954
No 43
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=28.42 E-value=11 Score=23.97 Aligned_cols=28 Identities=32% Similarity=0.711 Sum_probs=14.8
Q ss_pred cccccccccccCCCCceecCCCCCCccchhhhHh
Q 023560 199 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 232 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~ 232 (280)
.+.|..||.. |- ..+.|-...|.+||..
T Consensus 3 ~rfC~~CG~~---t~---~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAP---TK---PAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--B---EE---E-SSSS-EEESSSS-E
T ss_pred CcccCcCCcc---cc---CCCCcCEeECCCCcCE
Confidence 4679999983 22 2345666799999874
No 44
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=27.97 E-value=11 Score=24.50 Aligned_cols=33 Identities=30% Similarity=0.734 Sum_probs=19.9
Q ss_pred ccccccccccCCCCceecCCCCCCccchhhhHhH
Q 023560 200 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMW 233 (280)
Q Consensus 200 ~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~ 233 (280)
..|.+|++. -.-+..+.+..|....|-.||..|
T Consensus 3 ~~CP~C~~~-~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTS-FRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCE-EEeCHHHcCCCCCEEECCCCCCEE
Confidence 468888874 223333444455567888888654
No 45
>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=27.89 E-value=23 Score=23.74 Aligned_cols=31 Identities=29% Similarity=0.681 Sum_probs=19.1
Q ss_pred cccccccccccCCCCceecCCCCCCccchhhhH
Q 023560 199 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 231 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl 231 (280)
..+|..|++ ---|..+-...|..-.||-|+.
T Consensus 2 p~rC~~C~a--ylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRA--YLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT----BS-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCC--EECCcceEcCCCCEEECcCCCC
Confidence 467999998 5678877777876678999986
No 46
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=27.38 E-value=29 Score=22.51 Aligned_cols=29 Identities=24% Similarity=0.697 Sum_probs=19.6
Q ss_pred ccccccccccCCCCceecCCCCCCccchhhhH
Q 023560 200 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 231 (280)
Q Consensus 200 ~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl 231 (280)
-+|..|+.. -..|..-.++....|-.||.
T Consensus 6 y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHT---FEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCE---EEEEEecCCCCCCCCCCCCC
Confidence 479999982 34455443355678999997
No 47
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=26.84 E-value=29 Score=25.73 Aligned_cols=29 Identities=24% Similarity=0.716 Sum_probs=21.6
Q ss_pred cccccccccccCCCCceecCCCCCCccc-hhhhHhHHhcC
Q 023560 199 DIVCRHCGISEKSTPMMRRGPEGPRTLC-NACGLMWANKG 237 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LC-NACGl~~~~~g 237 (280)
-+.|.+||.+. | |+ +.+| ..|+.-|.++.
T Consensus 3 HkHC~~CG~~I---p-----~~--~~fCS~~C~~~~~k~q 32 (59)
T PF09889_consen 3 HKHCPVCGKPI---P-----PD--ESFCSPKCREEYRKRQ 32 (59)
T ss_pred CCcCCcCCCcC---C-----cc--hhhhCHHHHHHHHHHH
Confidence 46799999853 2 22 5899 59999888764
No 48
>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=26.76 E-value=51 Score=31.71 Aligned_cols=32 Identities=22% Similarity=0.621 Sum_probs=25.1
Q ss_pred ccccccccccCCCCceecCCCCCCccchhhhHhHHh
Q 023560 200 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWAN 235 (280)
Q Consensus 200 ~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~ 235 (280)
..|..|..+ ++.|--.-..+| +||+|--+-.+
T Consensus 2 ~~C~~C~~~-~t~p~i~fd~~G---vC~~C~~~~~~ 33 (343)
T TIGR03573 2 KFCKRCVMP-TTRPGITFDEDG---VCSACRNFEEK 33 (343)
T ss_pred CcCCCCCCC-CCCCCeeECCCC---CchhhhhHHhh
Confidence 579999997 466766667777 99999987643
No 49
>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=25.31 E-value=58 Score=26.36 Aligned_cols=44 Identities=25% Similarity=0.468 Sum_probs=33.5
Q ss_pred ccccccccccccCCCCceecCCCCCCccchhhhHhHHhcCC----CCCCCcC
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGT----LRDLSKA 245 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~~g~----~r~~~~~ 245 (280)
.+..|+.|+. .-|.|=.=.-| -.||-.|.-..+..|+ .|.++|.
T Consensus 2 ~N~~CaDC~~---~~p~w~s~~~G-ifvC~~CsgiHR~lg~his~VkSl~md 49 (112)
T smart00105 2 GNKKCFDCGA---PNPTWASVNLG-VFLCIECSGIHRSLGVHISKVRSLTLD 49 (112)
T ss_pred CCCcccCCCC---CCCCcEEeccc-eeEhHHhHHHHHhcCCCcCeeeecccC
Confidence 3578999998 35888888888 6899999988887764 4455543
No 50
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=24.15 E-value=35 Score=35.27 Aligned_cols=32 Identities=31% Similarity=0.669 Sum_probs=22.5
Q ss_pred cccccccccCCCCceecCCCCCCccchhhhHhHHhcC
Q 023560 201 VCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKG 237 (280)
Q Consensus 201 ~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~~~~~g 237 (280)
.|.||+.+ .+.-+ --.| -..|++||.-.-...
T Consensus 2 ~C~~C~~s---~fe~d-~a~g-~~~C~~CG~v~E~~~ 33 (521)
T KOG1598|consen 2 VCKNCGGS---NFERD-EATG-NLYCTACGTVLEYNN 33 (521)
T ss_pred cCCCCCCC---Ccccc-cccC-Cceeccccceeeccc
Confidence 69999983 45532 2345 699999999666554
No 51
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=22.63 E-value=50 Score=19.77 Aligned_cols=8 Identities=38% Similarity=1.215 Sum_probs=5.1
Q ss_pred ccchhhhH
Q 023560 224 TLCNACGL 231 (280)
Q Consensus 224 ~LCNACGl 231 (280)
.+|.-||.
T Consensus 14 ~fC~~CG~ 21 (23)
T PF13240_consen 14 KFCPNCGT 21 (23)
T ss_pred cchhhhCC
Confidence 56777764
No 52
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=22.58 E-value=39 Score=22.83 Aligned_cols=29 Identities=24% Similarity=0.587 Sum_probs=18.5
Q ss_pred ccccccccccCCCCceecCCCCCCccchhhhH
Q 023560 200 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 231 (280)
Q Consensus 200 ~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl 231 (280)
-+|..||. .--.|+..-+.....|-+||-
T Consensus 6 y~C~~Cg~---~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGH---EFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCC---EEEEEEEcCCCCCCcCCCCCC
Confidence 46899986 233344443444678999986
No 53
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=22.05 E-value=38 Score=23.86 Aligned_cols=29 Identities=31% Similarity=0.658 Sum_probs=17.1
Q ss_pred cccccccccccCCCCc-eecCCC---CCCc-cchhhhH
Q 023560 199 DIVCRHCGISEKSTPM-MRRGPE---GPRT-LCNACGL 231 (280)
Q Consensus 199 ~~~C~~Cg~~~~~Tp~-wR~Gp~---G~~~-LCNACGl 231 (280)
++.|..||. ++. ||++.+ +... .|..||-
T Consensus 1 LkPCPfCGg----~~~~~~~~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 1 LKPCPFCGG----ADVYLRRGFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCC----cceeeEeccCCCCCEEEEECCCCCC
Confidence 357999988 333 664322 2112 5888887
No 54
>PF14122 YokU: YokU-like protein
Probab=21.92 E-value=33 Score=27.43 Aligned_cols=16 Identities=19% Similarity=0.875 Sum_probs=12.3
Q ss_pred CccchhhhHhHHhcCC
Q 023560 223 RTLCNACGLMWANKGT 238 (280)
Q Consensus 223 ~~LCNACGl~~~~~g~ 238 (280)
...|+.||+-|....+
T Consensus 35 ~i~C~~CgmvYq~d~v 50 (87)
T PF14122_consen 35 AIICSNCGMVYQDDEV 50 (87)
T ss_pred eeeecCCCcEEehhHH
Confidence 3689999998876543
No 55
>PF15396 FAM60A: Protein Family FAM60A
Probab=21.74 E-value=47 Score=30.60 Aligned_cols=21 Identities=38% Similarity=0.503 Sum_probs=15.9
Q ss_pred ccchhhhHhHHhcCCCCCCCc
Q 023560 224 TLCNACGLMWANKGTLRDLSK 244 (280)
Q Consensus 224 ~LCNACGl~~~~~g~~r~~~~ 244 (280)
.+||||=|..++-.+|++-++
T Consensus 50 eICNACVLLVKRwKKLP~Gs~ 70 (213)
T PF15396_consen 50 EICNACVLLVKRWKKLPPGSK 70 (213)
T ss_pred hhhHHHHHHHHHHhhCCCCcc
Confidence 699999998888666555543
No 56
>PF12773 DZR: Double zinc ribbon
Probab=21.06 E-value=59 Score=22.10 Aligned_cols=28 Identities=29% Similarity=0.825 Sum_probs=17.2
Q ss_pred ccccccccccccCCCCceecCCCCCCccchhhhHh
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 232 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~ 232 (280)
...+|.+||+.. . .+.....+|..||-.
T Consensus 11 ~~~fC~~CG~~l--~-----~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 11 DAKFCPHCGTPL--P-----PPDQSKKICPNCGAE 38 (50)
T ss_pred cccCChhhcCCh--h-----hccCCCCCCcCCcCC
Confidence 457788888842 2 223334678888863
No 57
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=20.93 E-value=46 Score=22.92 Aligned_cols=29 Identities=24% Similarity=0.668 Sum_probs=19.9
Q ss_pred ccccccccccCCCCceecCCCCCCccchhhhH
Q 023560 200 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 231 (280)
Q Consensus 200 ~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl 231 (280)
-+|..|+. .--.|+.--+.....|-.||-
T Consensus 6 y~C~~Cg~---~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGH---RFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCC---EeEEEEecCCCCCCCCCCCCC
Confidence 57999997 344676533334578999997
No 58
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=20.63 E-value=21 Score=26.85 Aligned_cols=32 Identities=25% Similarity=0.441 Sum_probs=22.4
Q ss_pred ccccccccccCCCCc-eecCCCCCCccchhhhHhHH
Q 023560 200 IVCRHCGISEKSTPM-MRRGPEGPRTLCNACGLMWA 234 (280)
Q Consensus 200 ~~C~~Cg~~~~~Tp~-wR~Gp~G~~~LCNACGl~~~ 234 (280)
..|..|.+ .+|-. ||.. .-+..-|-+||-.-+
T Consensus 11 A~CP~C~~--~Dtl~mW~En-~ve~vECV~CG~~~~ 43 (66)
T COG3529 11 AVCPACQA--QDTLAMWREN-NVEIVECVKCGHHMR 43 (66)
T ss_pred CCCcccch--hhHHHHHHhc-CCceEehhhcchHhh
Confidence 46999999 45554 5554 444689999998553
No 59
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=20.62 E-value=43 Score=22.81 Aligned_cols=29 Identities=24% Similarity=0.654 Sum_probs=17.1
Q ss_pred cccccccccCCCCceecCCC-CCCccchhhhHhHH
Q 023560 201 VCRHCGISEKSTPMMRRGPE-GPRTLCNACGLMWA 234 (280)
Q Consensus 201 ~C~~Cg~~~~~Tp~wR~Gp~-G~~~LCNACGl~~~ 234 (280)
.|..||.- +-.+... .....|..||-.+.
T Consensus 2 FCp~Cg~~-----l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNM-----LIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCc-----cccccCCCCCEEECCcCCCeEE
Confidence 68899872 2222222 23578999996443
No 60
>PF09692 Arb1: Argonaute siRNA chaperone (ARC) complex subunit Arb1; InterPro: IPR018606 Arb1 is required for histone H3 Lys9 (H3-K9) methylation, heterochromatin, assembly and siRNA generation in fission yeast [].
Probab=20.43 E-value=68 Score=32.11 Aligned_cols=15 Identities=27% Similarity=0.572 Sum_probs=12.7
Q ss_pred HHH-HHHHHHHHHHhh
Q 023560 124 NRR-LASLIRFREKRK 138 (280)
Q Consensus 124 ~~R-~asl~r~~eKrk 138 (280)
.+| +.+|+|||.|||
T Consensus 46 ~~RiE~~IQRyr~rRR 61 (396)
T PF09692_consen 46 VERIEECIQRYRARRR 61 (396)
T ss_pred HHHHHHHHHHHHHhcC
Confidence 678 777999999986
No 61
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=20.01 E-value=40 Score=34.27 Aligned_cols=25 Identities=40% Similarity=0.949 Sum_probs=19.6
Q ss_pred ccccccccccccCCCCceecCCCCCCccchhhhHh
Q 023560 198 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 232 (280)
Q Consensus 198 ~~~~C~~Cg~~~~~Tp~wR~Gp~G~~~LCNACGl~ 232 (280)
....|.+||+ ..|.| .| -|.+||-|
T Consensus 6 t~f~C~~CG~---~s~KW----~G---kCp~Cg~W 30 (456)
T COG1066 6 TAFVCQECGY---VSPKW----LG---KCPACGAW 30 (456)
T ss_pred cEEEcccCCC---CCccc----cc---cCCCCCCc
Confidence 4578999998 67888 45 69999954
Done!