Query 026843
Match_columns 232
No_of_seqs 187 out of 774
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 13:30:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026843.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026843hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00320 GATA: GATA zinc finge 99.5 5.9E-15 1.3E-19 96.8 1.3 35 95-129 1-35 (36)
2 cd00202 ZnF_GATA Zinc finger D 99.5 1.9E-14 4.1E-19 102.2 2.6 37 94-130 1-37 (54)
3 smart00401 ZnF_GATA zinc finge 99.5 2.7E-14 5.8E-19 100.5 2.5 40 91-130 2-41 (52)
4 KOG1601 GATA-4/5/6 transcripti 98.7 1.1E-08 2.3E-13 84.4 2.3 37 92-128 199-235 (340)
5 COG5641 GAT1 GATA Zn-finger-co 97.8 8.1E-06 1.8E-10 80.1 1.1 42 90-131 156-201 (498)
6 KOG3554 Histone deacetylase co 84.1 0.82 1.8E-05 46.0 2.8 39 90-128 384-424 (693)
7 PF14803 Nudix_N_2: Nudix N-te 77.3 0.66 1.4E-05 30.5 -0.3 29 93-121 1-29 (34)
8 PF06203 CCT: CCT motif; Inte 74.7 1.4 3E-05 30.9 0.8 30 38-73 2-31 (45)
9 COG5347 GTPase-activating prot 67.5 2.5 5.3E-05 40.0 0.9 29 90-120 18-46 (319)
10 PF01412 ArfGap: Putative GTPa 65.6 5.6 0.00012 31.6 2.5 37 90-128 11-47 (116)
11 PRK03988 translation initiatio 64.4 2 4.3E-05 36.1 -0.3 31 91-122 101-131 (138)
12 COG5641 GAT1 GATA Zn-finger-co 63.8 3 6.6E-05 41.7 0.9 37 91-127 296-333 (498)
13 TIGR00311 aIF-2beta translatio 62.0 2.3 5E-05 35.4 -0.3 31 91-122 96-126 (133)
14 smart00653 eIF2B_5 domain pres 60.8 2.6 5.6E-05 34.1 -0.2 30 92-122 80-109 (110)
15 KOG3740 Uncharacterized conser 59.4 4 8.6E-05 42.2 0.8 33 90-122 460-495 (706)
16 smart00105 ArfGap Putative GTP 57.5 8.5 0.00018 30.4 2.2 35 91-127 2-36 (112)
17 PRK12336 translation initiatio 57.5 3 6.6E-05 36.5 -0.3 32 91-123 97-128 (201)
18 PLN03114 ADP-ribosylation fact 54.1 7.4 0.00016 38.0 1.6 31 90-122 20-50 (395)
19 PF04810 zf-Sec23_Sec24: Sec23 53.9 5.8 0.00013 26.3 0.6 31 92-122 2-32 (40)
20 PF01873 eIF-5_eIF-2B: Domain 48.8 4.9 0.00011 33.1 -0.4 28 93-121 94-121 (125)
21 PF06677 Auto_anti-p27: Sjogre 46.2 7.4 0.00016 26.5 0.2 25 92-121 17-41 (41)
22 PF08271 TF_Zn_Ribbon: TFIIB z 45.0 7.8 0.00017 25.7 0.2 26 94-122 2-27 (43)
23 PF12760 Zn_Tnp_IS1595: Transp 44.8 9.8 0.00021 25.7 0.6 30 89-121 15-44 (46)
24 PF09889 DUF2116: Uncharacteri 44.7 27 0.00058 25.6 3.0 33 92-132 3-36 (59)
25 PRK12286 rpmF 50S ribosomal pr 40.4 8.7 0.00019 27.8 -0.2 25 90-123 25-49 (57)
26 KOG0703 Predicted GTPase-activ 39.6 12 0.00026 35.2 0.6 29 90-120 23-51 (287)
27 KOG0706 Predicted GTPase-activ 37.1 14 0.0003 36.8 0.6 29 90-120 21-49 (454)
28 PF06689 zf-C4_ClpX: ClpX C4-t 35.6 16 0.00035 24.5 0.6 33 93-126 2-36 (41)
29 PF07282 OrfB_Zn_ribbon: Putat 34.3 21 0.00046 25.3 1.1 33 90-126 26-58 (69)
30 PRK14892 putative transcriptio 34.1 12 0.00025 30.0 -0.4 36 91-127 20-55 (99)
31 smart00778 Prim_Zn_Ribbon Zinc 33.6 25 0.00054 23.5 1.2 30 92-121 3-32 (37)
32 PRK00420 hypothetical protein; 33.0 19 0.00042 29.4 0.8 30 92-126 23-52 (112)
33 COG3952 Predicted membrane pro 32.8 11 0.00024 31.1 -0.7 19 105-125 76-94 (113)
34 PF11781 RRN7: RNA polymerase 29.9 24 0.00051 23.3 0.6 27 91-122 7-33 (36)
35 PF09723 Zn-ribbon_8: Zinc rib 29.3 16 0.00034 24.4 -0.3 29 93-122 6-34 (42)
36 COG3529 Predicted nucleic-acid 28.8 13 0.00028 28.0 -0.8 38 92-129 10-47 (66)
37 PLN03131 hypothetical protein; 28.8 29 0.00063 36.2 1.3 32 90-123 21-52 (705)
38 TIGR01385 TFSII transcription 28.8 16 0.00034 34.3 -0.5 36 90-125 256-297 (299)
39 PLN03119 putative ADP-ribosyla 28.8 29 0.00062 36.0 1.3 32 90-123 21-52 (648)
40 PF10083 DUF2321: Uncharacteri 28.5 30 0.00064 30.1 1.2 43 90-132 37-86 (158)
41 PF12773 DZR: Double zinc ribb 27.8 35 0.00076 22.8 1.2 27 91-122 11-37 (50)
42 PF13248 zf-ribbon_3: zinc-rib 26.8 41 0.00088 20.3 1.3 22 93-122 3-24 (26)
43 KOG1598 Transcription initiati 26.6 35 0.00075 34.7 1.4 51 93-147 1-55 (521)
44 smart00834 CxxC_CXXC_SSSS Puta 26.5 21 0.00046 22.7 -0.1 28 94-122 7-34 (41)
45 PRK00085 recO DNA repair prote 26.2 29 0.00062 30.1 0.7 31 90-121 147-177 (247)
46 PF01096 TFIIS_C: Transcriptio 26.1 4.4 9.5E-05 26.9 -3.4 31 94-124 2-38 (39)
47 COG2816 NPY1 NTP pyrophosphohy 26.1 25 0.00053 33.0 0.3 32 90-125 109-140 (279)
48 PRK00423 tfb transcription ini 25.9 27 0.00059 32.2 0.5 20 90-109 28-54 (310)
49 PF01783 Ribosomal_L32p: Ribos 24.7 16 0.00035 25.9 -0.9 22 91-121 25-46 (56)
50 COG4260 Membrane protease subu 24.5 39 0.00084 32.4 1.3 29 91-122 314-342 (345)
51 COG4869 PduL Propanediol utili 24.4 23 0.0005 31.7 -0.2 32 190-221 168-199 (210)
52 KOG0909 Peptide:N-glycanase [P 23.6 32 0.0007 34.6 0.6 34 89-122 158-202 (500)
53 smart00440 ZnF_C2C2 C2C2 Zinc 23.2 14 0.0003 24.6 -1.4 32 94-125 2-39 (40)
54 PF09526 DUF2387: Probable met 22.8 21 0.00045 26.9 -0.7 36 92-127 8-43 (71)
55 TIGR02605 CxxC_CxxC_SSSS putat 22.7 30 0.00065 23.3 0.1 29 93-122 6-34 (52)
56 COG0675 Transposase and inacti 22.1 36 0.00078 29.5 0.5 33 89-130 306-338 (364)
57 smart00659 RPOLCX RNA polymera 21.6 35 0.00076 23.4 0.3 30 93-127 3-32 (44)
58 COG1601 GCD7 Translation initi 21.5 30 0.00065 29.7 -0.1 34 90-124 103-136 (151)
59 PF15396 FAM60A: Protein Famil 21.4 52 0.0011 29.9 1.4 18 114-131 49-66 (213)
60 PHA02998 RNA polymerase subuni 20.6 28 0.0006 31.2 -0.5 36 91-126 142-183 (195)
61 PRK08351 DNA-directed RNA poly 20.3 64 0.0014 23.9 1.4 15 94-108 17-32 (61)
No 1
>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=99.49 E-value=5.9e-15 Score=96.80 Aligned_cols=35 Identities=57% Similarity=1.230 Sum_probs=28.2
Q ss_pred ccCCCCCCCCcccCCCCCCcccchHHHHHHHHhhh
Q 026843 95 CSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARK 129 (232)
Q Consensus 95 C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~k~r~ 129 (232)
|++|++++||+||+||.|+.+|||+||++|++.++
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 89999999999999999988899999999998764
No 2
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.47 E-value=1.9e-14 Score=102.23 Aligned_cols=37 Identities=57% Similarity=1.149 Sum_probs=34.1
Q ss_pred cccCCCCCCCCcccCCCCCCcccchHHHHHHHHhhhH
Q 026843 94 ICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARKA 130 (232)
Q Consensus 94 ~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~k~r~~ 130 (232)
+|+||++++||+||+||+|..+|||||||+|++....
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~ 37 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVM 37 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCCC
Confidence 5999999999999999988899999999999988643
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.46 E-value=2.7e-14 Score=100.48 Aligned_cols=40 Identities=55% Similarity=1.098 Sum_probs=36.5
Q ss_pred CCccccCCCCCCCCcccCCCCCCcccchHHHHHHHHhhhH
Q 026843 91 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARKA 130 (232)
Q Consensus 91 ~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~k~r~~ 130 (232)
..+.|++|++++||+||+||.|+.+|||||||+|++....
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 4678999999999999999999889999999999987654
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.66 E-value=1.1e-08 Score=84.44 Aligned_cols=37 Identities=68% Similarity=1.399 Sum_probs=35.2
Q ss_pred CccccCCCCCCCCcccCCCCCCcccchHHHHHHHHhh
Q 026843 92 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKAR 128 (232)
Q Consensus 92 ~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~k~r 128 (232)
...|.+|+++.||+||+++.|+..+|||||++|++..
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~ 235 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGG 235 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcC
Confidence 5899999999999999999999999999999999984
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=97.76 E-value=8.1e-06 Score=80.15 Aligned_cols=42 Identities=40% Similarity=0.872 Sum_probs=34.6
Q ss_pred CCCccccCCCCCCCCcccCCCCC----CcccchHHHHHHHHhhhHH
Q 026843 90 NTVRICSDCNTTTTPLWRSGPRG----PKSLCNACGIRQRKARKAM 131 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRrGP~G----~~~LCNACGL~~~k~r~~~ 131 (232)
....+|.+|.++.||+|||++.+ +-+|||||||+|+-.....
T Consensus 156 ~~~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r 201 (498)
T COG5641 156 NQPHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPR 201 (498)
T ss_pred cccchhccccccCCccccccccccccCCccccccccccccccCCcC
Confidence 34559999999999999999993 3789999999998654443
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=84.07 E-value=0.82 Score=45.99 Aligned_cols=39 Identities=31% Similarity=0.555 Sum_probs=32.1
Q ss_pred CCCccccCCCCCCCCcc--cCCCCCCcccchHHHHHHHHhh
Q 026843 90 NTVRICSDCNTTTTPLW--RSGPRGPKSLCNACGIRQRKAR 128 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~W--RrGP~G~~~LCNACGL~~~k~r 128 (232)
...+.|-+|+|+++-+| ..+|+-...||-.|=++|+|..
T Consensus 384 ~~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKyg 424 (693)
T KOG3554|consen 384 QDGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYG 424 (693)
T ss_pred CCCCcccccccccccceeccCCCCccchhhHHHHHHHHHhc
Confidence 34789999999999999 3455566679999999999964
No 7
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=77.26 E-value=0.66 Score=30.47 Aligned_cols=29 Identities=24% Similarity=0.667 Sum_probs=15.7
Q ss_pred ccccCCCCCCCCcccCCCCCCcccchHHH
Q 026843 93 RICSDCNTTTTPLWRSGPRGPKSLCNACG 121 (232)
Q Consensus 93 ~~C~~Cgtt~TP~WRrGP~G~~~LCNACG 121 (232)
+.|.+||..-+-.--.|.+-.+.+|.+||
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACG 29 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTT
T ss_pred CccccccChhhhhcCCCCCccceECCCCC
Confidence 35999998754333367777788999998
No 8
>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=74.74 E-value=1.4 Score=30.86 Aligned_cols=30 Identities=7% Similarity=0.085 Sum_probs=25.4
Q ss_pred chhhhhHHHHhhcCCCCCCCCccchhhHHHHhhhcc
Q 026843 38 MSSKMRLANKIINSSSVSTGTHDESVKVAEKLLHEH 73 (232)
Q Consensus 38 m~skmR~~~K~~~~~~~~e~~~dKkir~~v~~~~~q 73 (232)
..+++|+.+| +..++|+|+|+|.+++....
T Consensus 2 ~~~l~Ry~~K------r~~R~f~kkirY~~Rk~~A~ 31 (45)
T PF06203_consen 2 EEKLQRYREK------RKRRNFEKKIRYESRKAVAD 31 (45)
T ss_pred HHHHHHHHHH------HHhhcccccCCcchHHHHHh
Confidence 3578999999 78899999999999986544
No 9
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=67.46 E-value=2.5 Score=40.01 Aligned_cols=29 Identities=34% Similarity=0.838 Sum_probs=26.7
Q ss_pred CCCccccCCCCCCCCcccCCCCCCcccchHH
Q 026843 90 NTVRICSDCNTTTTPLWRSGPRGPKSLCNAC 120 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRrGP~G~~~LCNAC 120 (232)
.....|.+|++.. |.|-.-.-| ..||-.|
T Consensus 18 ~~Nk~CaDCga~~-P~W~S~nlG-vfiCi~C 46 (319)
T COG5347 18 SSNKKCADCGAPN-PTWASVNLG-VFLCIDC 46 (319)
T ss_pred cccCccccCCCCC-CceEecccC-eEEEeec
Confidence 4567899999999 999999999 8999999
No 10
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=65.60 E-value=5.6 Score=31.61 Aligned_cols=37 Identities=30% Similarity=0.632 Sum_probs=25.9
Q ss_pred CCCccccCCCCCCCCcccCCCCCCcccchHHHHHHHHhh
Q 026843 90 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKAR 128 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~k~r 128 (232)
...+.|++|+... |.|-.-.-| -.||-.|.-.++...
T Consensus 11 ~~N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~lg 47 (116)
T PF01412_consen 11 PGNKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRSLG 47 (116)
T ss_dssp TTCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHHHT
T ss_pred cCcCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHHhc
Confidence 5568899999655 599999999 799999987777653
No 11
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=64.39 E-value=2 Score=36.06 Aligned_cols=31 Identities=32% Similarity=0.660 Sum_probs=23.5
Q ss_pred CCccccCCCCCCCCcccCCCCCCcccchHHHH
Q 026843 91 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 122 (232)
Q Consensus 91 ~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL 122 (232)
.--.|..|+...|-+=+.+-.- -.-|+|||-
T Consensus 101 ~yVlC~~C~spdT~l~k~~r~~-~l~C~ACGa 131 (138)
T PRK03988 101 EYVICPECGSPDTKLIKEGRIW-VLKCEACGA 131 (138)
T ss_pred hcEECCCCCCCCcEEEEcCCeE-EEEcccCCC
Confidence 3467999999999887753322 458999994
No 12
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=63.84 E-value=3 Score=41.71 Aligned_cols=37 Identities=32% Similarity=0.478 Sum_probs=29.7
Q ss_pred CCccccCCCC-CCCCcccCCCCCCcccchHHHHHHHHh
Q 026843 91 TVRICSDCNT-TTTPLWRSGPRGPKSLCNACGIRQRKA 127 (232)
Q Consensus 91 ~~~~C~~Cgt-t~TP~WRrGP~G~~~LCNACGL~~~k~ 127 (232)
....|.+|.+ +.||.||+...-.-++||+||+..+..
T Consensus 296 s~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~ 333 (498)
T COG5641 296 SDKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPP 333 (498)
T ss_pred hhcCcccccccccCcccccccccccccccccccccCCc
Confidence 3667888887 789999998877689999999876543
No 13
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=62.01 E-value=2.3 Score=35.43 Aligned_cols=31 Identities=32% Similarity=0.706 Sum_probs=23.1
Q ss_pred CCccccCCCCCCCCcccCCCCCCcccchHHHH
Q 026843 91 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 122 (232)
Q Consensus 91 ~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL 122 (232)
.--.|..|+...|-+-+.+.-- -.-|+|||-
T Consensus 96 ~yVlC~~C~sPdT~l~k~~r~~-~l~C~ACGa 126 (133)
T TIGR00311 96 KYVICRECNRPDTRIIKEGRVS-LLKCEACGA 126 (133)
T ss_pred heEECCCCCCCCcEEEEeCCeE-EEecccCCC
Confidence 3467999999999888753322 348999994
No 14
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=60.83 E-value=2.6 Score=34.07 Aligned_cols=30 Identities=27% Similarity=0.574 Sum_probs=22.6
Q ss_pred CccccCCCCCCCCcccCCCCCCcccchHHHH
Q 026843 92 VRICSDCNTTTTPLWRSGPRGPKSLCNACGI 122 (232)
Q Consensus 92 ~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL 122 (232)
--.|..|+..+|-+=+.+..- -.-|+|||-
T Consensus 80 yVlC~~C~spdT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 80 YVLCPECGSPDTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred cEECCCCCCCCcEEEEeCCeE-EEEccccCC
Confidence 467999999999888873322 346999994
No 15
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=59.36 E-value=4 Score=42.22 Aligned_cols=33 Identities=24% Similarity=0.656 Sum_probs=27.9
Q ss_pred CCCccccCCCCCCCCcccCCCCC---CcccchHHHH
Q 026843 90 NTVRICSDCNTTTTPLWRSGPRG---PKSLCNACGI 122 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRrGP~G---~~~LCNACGL 122 (232)
.+.-.|..|.|.-||.|+.-+.+ ++.+|.+|-.
T Consensus 460 ~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvt 495 (706)
T KOG3740|consen 460 TEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVT 495 (706)
T ss_pred CCchhhhhcccccccccccccccCcchHHHHHhhhh
Confidence 45788999999999999987766 5679999954
No 16
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=57.50 E-value=8.5 Score=30.44 Aligned_cols=35 Identities=31% Similarity=0.611 Sum_probs=29.4
Q ss_pred CCccccCCCCCCCCcccCCCCCCcccchHHHHHHHHh
Q 026843 91 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKA 127 (232)
Q Consensus 91 ~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~k~ 127 (232)
+...|++|+. .-|.|-.-.-| ..||-.|.-..+..
T Consensus 2 ~N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~l 36 (112)
T smart00105 2 GNKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRSL 36 (112)
T ss_pred CCCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHhc
Confidence 3678999998 55999999999 78999998777754
No 17
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=57.45 E-value=3 Score=36.55 Aligned_cols=32 Identities=31% Similarity=0.572 Sum_probs=23.9
Q ss_pred CCccccCCCCCCCCcccCCCCCCcccchHHHHH
Q 026843 91 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGIR 123 (232)
Q Consensus 91 ~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~ 123 (232)
.--.|..|+...|-+-+.+..- -.-|+|||-.
T Consensus 97 ~yV~C~~C~~pdT~l~k~~~~~-~l~C~aCGa~ 128 (201)
T PRK12336 97 EYVICSECGLPDTRLVKEDRVL-MLRCDACGAH 128 (201)
T ss_pred heEECCCCCCCCcEEEEcCCeE-EEEcccCCCC
Confidence 3467999999999887764322 3489999954
No 18
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=54.06 E-value=7.4 Score=38.01 Aligned_cols=31 Identities=39% Similarity=0.834 Sum_probs=26.4
Q ss_pred CCCccccCCCCCCCCcccCCCCCCcccchHHHH
Q 026843 90 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 122 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL 122 (232)
...+.|.+|+... |.|-.-.-| ..||..|.=
T Consensus 20 PgNk~CaDCga~n-PtWASvn~G-IFLCl~CSG 50 (395)
T PLN03114 20 SDNKICFDCNAKN-PTWASVTYG-IFLCIDCSA 50 (395)
T ss_pred cCCCcCccCCCCC-CCceeeccc-eeehhhhhH
Confidence 4577899999875 999999999 799999943
No 19
>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=53.88 E-value=5.8 Score=26.32 Aligned_cols=31 Identities=26% Similarity=0.606 Sum_probs=21.2
Q ss_pred CccccCCCCCCCCcccCCCCCCcccchHHHH
Q 026843 92 VRICSDCNTTTTPLWRSGPRGPKSLCNACGI 122 (232)
Q Consensus 92 ~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL 122 (232)
..+|.+|++---|.-.=...|....||-|+.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCC
Confidence 5689999999999988888887889999985
No 20
>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=48.78 E-value=4.9 Score=33.08 Aligned_cols=28 Identities=32% Similarity=0.718 Sum_probs=22.9
Q ss_pred ccccCCCCCCCCcccCCCCCCcccchHHH
Q 026843 93 RICSDCNTTTTPLWRSGPRGPKSLCNACG 121 (232)
Q Consensus 93 ~~C~~Cgtt~TP~WRrGP~G~~~LCNACG 121 (232)
-.|..|+..+|-+=+.+..- -.-|+|||
T Consensus 94 VlC~~C~spdT~l~k~~r~~-~l~C~aCG 121 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLI-FLKCKACG 121 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCC-EEEETTTS
T ss_pred EEcCCCCCCccEEEEcCCEE-EEEecccC
Confidence 57999999999888774444 46899998
No 21
>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=46.18 E-value=7.4 Score=26.53 Aligned_cols=25 Identities=48% Similarity=1.010 Sum_probs=19.0
Q ss_pred CccccCCCCCCCCcccCCCCCCcccchHHH
Q 026843 92 VRICSDCNTTTTPLWRSGPRGPKSLCNACG 121 (232)
Q Consensus 92 ~~~C~~Cgtt~TP~WRrGP~G~~~LCNACG 121 (232)
...|..| .||+.| ..+| ..+|-+|+
T Consensus 17 ~~~Cp~C---~~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDC---GTPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred cCccCCC---CCeeEE-ecCC-CEECCCCC
Confidence 4468888 489999 4466 68999985
No 22
>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=44.97 E-value=7.8 Score=25.73 Aligned_cols=26 Identities=27% Similarity=0.897 Sum_probs=13.4
Q ss_pred cccCCCCCCCCcccCCCCCCcccchHHHH
Q 026843 94 ICSDCNTTTTPLWRSGPRGPKSLCNACGI 122 (232)
Q Consensus 94 ~C~~Cgtt~TP~WRrGP~G~~~LCNACGL 122 (232)
.|.+|+++. -.+ ....| ..+|..||+
T Consensus 2 ~Cp~Cg~~~-~~~-D~~~g-~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKE-IVF-DPERG-ELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSE-EEE-ETTTT-EEEETTT-B
T ss_pred CCcCCcCCc-eEE-cCCCC-eEECCCCCC
Confidence 477777755 122 22334 457777774
No 23
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=44.79 E-value=9.8 Score=25.69 Aligned_cols=30 Identities=27% Similarity=0.552 Sum_probs=21.4
Q ss_pred CCCCccccCCCCCCCCcccCCCCCCcccchHHH
Q 026843 89 NNTVRICSDCNTTTTPLWRSGPRGPKSLCNACG 121 (232)
Q Consensus 89 ~~~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACG 121 (232)
+....+|.+|+.+ ...|-++ .+ ..-|++|+
T Consensus 15 W~~g~~CP~Cg~~-~~~~~~~-~~-~~~C~~C~ 44 (46)
T PF12760_consen 15 WPDGFVCPHCGST-KHYRLKT-RG-RYRCKACR 44 (46)
T ss_pred CCCCCCCCCCCCe-eeEEeCC-CC-eEECCCCC
Confidence 3445779999998 5555555 33 67999996
No 24
>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=44.67 E-value=27 Score=25.61 Aligned_cols=33 Identities=30% Similarity=0.668 Sum_probs=25.6
Q ss_pred CccccCCCCCCCCcccCCCCCCcccc-hHHHHHHHHhhhHHH
Q 026843 92 VRICSDCNTTTTPLWRSGPRGPKSLC-NACGIRQRKARKAMQ 132 (232)
Q Consensus 92 ~~~C~~Cgtt~TP~WRrGP~G~~~LC-NACGL~~~k~r~~~~ 132 (232)
-+.|.+||...-| + ...| ..|+--|.+.++.+.
T Consensus 3 HkHC~~CG~~Ip~-------~-~~fCS~~C~~~~~k~qk~~~ 36 (59)
T PF09889_consen 3 HKHCPVCGKPIPP-------D-ESFCSPKCREEYRKRQKRMR 36 (59)
T ss_pred CCcCCcCCCcCCc-------c-hhhhCHHHHHHHHHHHHHHH
Confidence 4679999977654 2 6799 599999999887653
No 25
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=40.42 E-value=8.7 Score=27.78 Aligned_cols=25 Identities=24% Similarity=0.760 Sum_probs=19.8
Q ss_pred CCCccccCCCCCCCCcccCCCCCCcccchHHHHH
Q 026843 90 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGIR 123 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~ 123 (232)
...-.|.+||...-| +.+|..||.|
T Consensus 25 ~~l~~C~~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 25 PGLVECPNCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred CcceECCCCCCccCC---------eEECCCCCcC
Confidence 456779999987765 7899999954
No 26
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=39.57 E-value=12 Score=35.22 Aligned_cols=29 Identities=31% Similarity=0.803 Sum_probs=25.8
Q ss_pred CCCccccCCCCCCCCcccCCCCCCcccchHH
Q 026843 90 NTVRICSDCNTTTTPLWRSGPRGPKSLCNAC 120 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRrGP~G~~~LCNAC 120 (232)
...+.|++|++. .|.|-.---| ..+|-.|
T Consensus 23 ~~N~~CADC~a~-~P~WaSwnlG-vFiC~~C 51 (287)
T KOG0703|consen 23 PDNKVCADCGAK-GPRWASWNLG-VFICLRC 51 (287)
T ss_pred cccCcccccCCC-CCCeEEeecC-eEEEeec
Confidence 347889999999 9999998889 7899999
No 27
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=37.12 E-value=14 Score=36.82 Aligned_cols=29 Identities=34% Similarity=0.846 Sum_probs=26.0
Q ss_pred CCCccccCCCCCCCCcccCCCCCCcccchHH
Q 026843 90 NTVRICSDCNTTTTPLWRSGPRGPKSLCNAC 120 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRrGP~G~~~LCNAC 120 (232)
...++|.+|+.. .|-|-.-+.| -.||--|
T Consensus 21 ~~NKvCFDCgAk-nPtWaSVTYG-IFLCiDC 49 (454)
T KOG0706|consen 21 SENKVCFDCGAK-NPTWASVTYG-IFLCIDC 49 (454)
T ss_pred CCCceecccCCC-CCCceeecce-EEEEEec
Confidence 567899999975 5999999999 8999999
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=35.65 E-value=16 Score=24.45 Aligned_cols=33 Identities=27% Similarity=0.653 Sum_probs=20.1
Q ss_pred ccccCCCCCCCCc--ccCCCCCCcccchHHHHHHHH
Q 026843 93 RICSDCNTTTTPL--WRSGPRGPKSLCNACGIRQRK 126 (232)
Q Consensus 93 ~~C~~Cgtt~TP~--WRrGP~G~~~LCNACGL~~~k 126 (232)
+.|+-||.+.+.. .=.||+| ..+|+.|-..-..
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~-~~IC~~Cv~~~~~ 36 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNG-AYICDECVEQAYE 36 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-S-EEEEHHHHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCC-cEECHHHHHHHHH
Confidence 5799999987633 2378877 6899999765443
No 29
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=34.31 E-value=21 Score=25.28 Aligned_cols=33 Identities=21% Similarity=0.536 Sum_probs=23.5
Q ss_pred CCCccccCCCCCCCCcccCCCCCCcccchHHHHHHHH
Q 026843 90 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRK 126 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~k 126 (232)
.....|..||...-- ...+....|..||..+..
T Consensus 26 ~TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 26 YTSQTCPRCGHRNKK----RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CCccCccCccccccc----ccccceEEcCCCCCEECc
Confidence 356679999987654 445556799999986543
No 30
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=34.09 E-value=12 Score=30.01 Aligned_cols=36 Identities=14% Similarity=0.307 Sum_probs=23.1
Q ss_pred CCccccCCCCCCCCcccCCCCCCcccchHHHHHHHHh
Q 026843 91 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKA 127 (232)
Q Consensus 91 ~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~k~ 127 (232)
..-.|.+|+.. +-.-..+-..++..|..||.++...
T Consensus 20 t~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 20 KIFECPRCGKV-SISVKIKKNIAIITCGNCGLYTEFE 55 (99)
T ss_pred cEeECCCCCCe-EeeeecCCCcceEECCCCCCccCEE
Confidence 35569999953 3222222245588999999987653
No 31
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=33.60 E-value=25 Score=23.50 Aligned_cols=30 Identities=17% Similarity=0.472 Sum_probs=20.8
Q ss_pred CccccCCCCCCCCcccCCCCCCcccchHHH
Q 026843 92 VRICSDCNTTTTPLWRSGPRGPKSLCNACG 121 (232)
Q Consensus 92 ~~~C~~Cgtt~TP~WRrGP~G~~~LCNACG 121 (232)
...|-.|+.+..=.|..........|+.||
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg 32 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRGTWFCSVCG 32 (37)
T ss_pred ccCCCCCCCccccccccCCCCcCEEeCCCC
Confidence 346999998876667553332268999996
No 32
>PRK00420 hypothetical protein; Validated
Probab=33.02 E-value=19 Score=29.41 Aligned_cols=30 Identities=23% Similarity=0.516 Sum_probs=22.5
Q ss_pred CccccCCCCCCCCcccCCCCCCcccchHHHHHHHH
Q 026843 92 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRK 126 (232)
Q Consensus 92 ~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~k 126 (232)
...|..|| +|+.|- ..| ...|-.||-.+.-
T Consensus 23 ~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCC---Ccceec-CCC-ceECCCCCCeeee
Confidence 35699998 688875 555 6899999986653
No 33
>COG3952 Predicted membrane protein [Function unknown]
Probab=32.76 E-value=11 Score=31.06 Aligned_cols=19 Identities=32% Similarity=0.434 Sum_probs=14.6
Q ss_pred cccCCCCCCcccchHHHHHHH
Q 026843 105 LWRSGPRGPKSLCNACGIRQR 125 (232)
Q Consensus 105 ~WRrGP~G~~~LCNACGL~~~ 125 (232)
+||.+|-+ .||++||++..
T Consensus 76 i~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HHhcchHH--HHHHhhhHHHH
Confidence 46777777 69999999753
No 34
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=29.95 E-value=24 Score=23.27 Aligned_cols=27 Identities=26% Similarity=0.701 Sum_probs=20.4
Q ss_pred CCccccCCCCCCCCcccCCCCCCcccchHHHH
Q 026843 91 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 122 (232)
Q Consensus 91 ~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL 122 (232)
....|..|+.. |-...+| ...|..||-
T Consensus 7 ~~~~C~~C~~~----~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 7 PNEPCPVCGSR----WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CCCcCCCCCCe----EeEccCC-EEEhhhCce
Confidence 34459999987 6667778 789999983
No 35
>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=29.30 E-value=16 Score=24.39 Aligned_cols=29 Identities=21% Similarity=0.452 Sum_probs=17.3
Q ss_pred ccccCCCCCCCCcccCCCCCCcccchHHHH
Q 026843 93 RICSDCNTTTTPLWRSGPRGPKSLCNACGI 122 (232)
Q Consensus 93 ~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL 122 (232)
-.|..||..-+-+..-.. .....|-+||-
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 357888866553333333 44567888875
No 36
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=28.83 E-value=13 Score=27.97 Aligned_cols=38 Identities=24% Similarity=0.390 Sum_probs=28.9
Q ss_pred CccccCCCCCCCCcccCCCCCCcccchHHHHHHHHhhh
Q 026843 92 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARK 129 (232)
Q Consensus 92 ~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~k~r~ 129 (232)
...|..|.+..|-.|.+...-+..-|-+||-..+..-+
T Consensus 10 GA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~~~~k 47 (66)
T COG3529 10 GAVCPACQAQDTLAMWRENNVEIVECVKCGHHMREADK 47 (66)
T ss_pred cCCCcccchhhHHHHHHhcCCceEehhhcchHhhhccH
Confidence 45699999999877655555557899999988765443
No 37
>PLN03131 hypothetical protein; Provisional
Probab=28.80 E-value=29 Score=36.25 Aligned_cols=32 Identities=22% Similarity=0.408 Sum_probs=26.5
Q ss_pred CCCccccCCCCCCCCcccCCCCCCcccchHHHHH
Q 026843 90 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGIR 123 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~ 123 (232)
.+.+.|.+|+... |.|-.-.-| ..+|-.|.=.
T Consensus 21 PgNk~CADCga~~-P~WASiNlG-IFICi~CSGI 52 (705)
T PLN03131 21 PPNRRCINCNSLG-PQFVCTNFW-TFICMTCSGI 52 (705)
T ss_pred cCCCccccCCCCC-CCeeEeccc-eEEchhchhh
Confidence 5678899999755 999998889 7899999443
No 38
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=28.78 E-value=16 Score=34.27 Aligned_cols=36 Identities=22% Similarity=0.560 Sum_probs=25.2
Q ss_pred CCCccccCCCCCCCCcc----cCCCCCCc--ccchHHHHHHH
Q 026843 90 NTVRICSDCNTTTTPLW----RSGPRGPK--SLCNACGIRQR 125 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~W----RrGP~G~~--~LCNACGL~~~ 125 (232)
.....|..|+-...-.| |.+.++-. +.|..||-+|+
T Consensus 256 t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 256 TDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 44678999998776555 44444422 38999998885
No 39
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=28.77 E-value=29 Score=35.96 Aligned_cols=32 Identities=25% Similarity=0.432 Sum_probs=26.7
Q ss_pred CCCccccCCCCCCCCcccCCCCCCcccchHHHHH
Q 026843 90 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGIR 123 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~ 123 (232)
.+.+.|.+|+... |.|-.-.-| ..+|-.|.=.
T Consensus 21 PgNk~CADCgs~~-P~WASiNlG-IFICi~CSGI 52 (648)
T PLN03119 21 PPNRRCINCNSLG-PQYVCTTFW-TFVCMACSGI 52 (648)
T ss_pred cCCCccccCCCCC-CCceeeccc-eEEeccchhh
Confidence 5568899999866 999999999 7899999443
No 40
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=28.54 E-value=30 Score=30.14 Aligned_cols=43 Identities=23% Similarity=0.510 Sum_probs=27.8
Q ss_pred CCCccccCCCCCCCCcccC-------CCCCCcccchHHHHHHHHhhhHHH
Q 026843 90 NTVRICSDCNTTTTPLWRS-------GPRGPKSLCNACGIRQRKARKAMQ 132 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRr-------GP~G~~~LCNACGL~~~k~r~~~~ 132 (232)
.....|.+|.+..--.|-- ++......|+.||..|=-...+.+
T Consensus 37 ~tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPWt~~~L~ 86 (158)
T PF10083_consen 37 KTITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPWTENALE 86 (158)
T ss_pred HHHHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCchHHHHHH
Confidence 3567788888876444533 444556799999998754444433
No 41
>PF12773 DZR: Double zinc ribbon
Probab=27.79 E-value=35 Score=22.77 Aligned_cols=27 Identities=30% Similarity=0.842 Sum_probs=14.0
Q ss_pred CCccccCCCCCCCCcccCCCCCCcccchHHHH
Q 026843 91 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 122 (232)
Q Consensus 91 ~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL 122 (232)
....|.+||+.-. .+......|..||-
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGA 37 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcC
Confidence 3556666666555 22222345666654
No 42
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=26.76 E-value=41 Score=20.28 Aligned_cols=22 Identities=27% Similarity=0.880 Sum_probs=13.3
Q ss_pred ccccCCCCCCCCcccCCCCCCcccchHHHH
Q 026843 93 RICSDCNTTTTPLWRSGPRGPKSLCNACGI 122 (232)
Q Consensus 93 ~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL 122 (232)
+.|.+||+...+. ...|..||.
T Consensus 3 ~~Cp~Cg~~~~~~--------~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPD--------AKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcc--------cccChhhCC
Confidence 4688888754322 346777764
No 43
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=26.62 E-value=35 Score=34.69 Aligned_cols=51 Identities=20% Similarity=0.407 Sum_probs=29.5
Q ss_pred ccccCCCCCCCCcccCCCCCCcccchHHHHHHHHhhhH----HHHHHhcCCeeccCCCc
Q 026843 93 RICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARKA----MQAAAESGTTTAKDNSS 147 (232)
Q Consensus 93 ~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~k~r~~----~~~~~~~g~~~~~~~ss 147 (232)
+.|.||+.+. +. |+.-.| ...|++||.-.....-. +-.. ..|.++....+.
T Consensus 1 ~~C~~C~~s~-fe-~d~a~g-~~~C~~CG~v~E~~~ivsev~F~e~-~~G~~v~~~~~g 55 (521)
T KOG1598|consen 1 MVCKNCGGSN-FE-RDEATG-NLYCTACGTVLEYNNIVAEVTFVEG-AQGQFVRVGQSG 55 (521)
T ss_pred CcCCCCCCCC-cc-cccccC-CceeccccceeeccceeEEeeeecc-cceeEEeccccC
Confidence 4699999864 12 223445 68999999865432111 1111 567777665543
No 44
>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=26.49 E-value=21 Score=22.66 Aligned_cols=28 Identities=29% Similarity=0.640 Sum_probs=17.5
Q ss_pred cccCCCCCCCCcccCCCCCCcccchHHHH
Q 026843 94 ICSDCNTTTTPLWRSGPRGPKSLCNACGI 122 (232)
Q Consensus 94 ~C~~Cgtt~TP~WRrGP~G~~~LCNACGL 122 (232)
.|..|+..-+ .|..-..+....|..||-
T Consensus 7 ~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFE-VLQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEE-EEEecCCCCCCCCCCCCC
Confidence 5888887554 333333344567888886
No 45
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=26.25 E-value=29 Score=30.06 Aligned_cols=31 Identities=23% Similarity=0.585 Sum_probs=25.4
Q ss_pred CCCccccCCCCCCCCcccCCCCCCcccchHHH
Q 026843 90 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACG 121 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACG 121 (232)
.....|..||......|-.-++| ..+|..|+
T Consensus 147 p~l~~C~~Cg~~~~~~~f~~~~g-g~~c~~c~ 177 (247)
T PRK00085 147 LDLDHCAVCGAPGDHRYFSPKEG-GAVCSECG 177 (247)
T ss_pred cchhhHhcCCCCCCceEEecccC-Cccccccc
Confidence 45568999998877677777777 78999997
No 46
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=26.13 E-value=4.4 Score=26.87 Aligned_cols=31 Identities=26% Similarity=0.614 Sum_probs=17.0
Q ss_pred cccCCCCCCCCcc----cCCCCCCc--ccchHHHHHH
Q 026843 94 ICSDCNTTTTPLW----RSGPRGPK--SLCNACGIRQ 124 (232)
Q Consensus 94 ~C~~Cgtt~TP~W----RrGP~G~~--~LCNACGL~~ 124 (232)
.|..|+...+-.| |+++++.. ..|..||-+|
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 4778887764333 56666532 3688887544
No 47
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=26.06 E-value=25 Score=33.02 Aligned_cols=32 Identities=31% Similarity=0.661 Sum_probs=23.9
Q ss_pred CCCccccCCCCCCCCcccCCCCCCcccchHHHHHHH
Q 026843 90 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQR 125 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~ 125 (232)
...+-|..||+...|. ..|-+.+|+.||.++-
T Consensus 109 ~~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~f 140 (279)
T COG2816 109 RSHRFCGRCGTKTYPR----EGGWARVCPKCGHEHF 140 (279)
T ss_pred hhCcCCCCCCCcCccc----cCceeeeCCCCCCccC
Confidence 4578899999987763 3455679999998653
No 48
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=25.91 E-value=27 Score=32.21 Aligned_cols=20 Identities=30% Similarity=0.740 Sum_probs=12.1
Q ss_pred CCCccccCCCC-------CCCCcccCC
Q 026843 90 NTVRICSDCNT-------TTTPLWRSG 109 (232)
Q Consensus 90 ~~~~~C~~Cgt-------t~TP~WRrG 109 (232)
.+..+|.+||. ...|+||.=
T Consensus 28 ~Ge~vC~~CG~Vl~e~~iD~g~EWR~f 54 (310)
T PRK00423 28 RGEIVCADCGLVIEENIIDQGPEWRAF 54 (310)
T ss_pred CCeEeecccCCcccccccccCCCccCC
Confidence 45666777775 246677653
No 49
>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=24.71 E-value=16 Score=25.92 Aligned_cols=22 Identities=27% Similarity=0.948 Sum_probs=16.8
Q ss_pred CCccccCCCCCCCCcccCCCCCCcccchHHH
Q 026843 91 TVRICSDCNTTTTPLWRSGPRGPKSLCNACG 121 (232)
Q Consensus 91 ~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACG 121 (232)
....|.+||...- ++.+|.+||
T Consensus 25 ~l~~c~~cg~~~~---------~H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKL---------PHRVCPSCG 46 (56)
T ss_dssp SEEESSSSSSEES---------TTSBCTTTB
T ss_pred ceeeeccCCCEec---------ccEeeCCCC
Confidence 4678999996433 378999999
No 50
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=24.49 E-value=39 Score=32.45 Aligned_cols=29 Identities=28% Similarity=0.748 Sum_probs=21.6
Q ss_pred CCccccCCCCCCCCcccCCCCCCcccchHHHH
Q 026843 91 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 122 (232)
Q Consensus 91 ~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL 122 (232)
....|.+||...|+-.-.|. .-.|-+||-
T Consensus 314 k~nfc~ncG~~~t~~~~ng~---a~fcp~cgq 342 (345)
T COG4260 314 KLNFCLNCGCGTTADFDNGK---AKFCPECGQ 342 (345)
T ss_pred ccccccccCcccccCCccch---hhhChhhcC
Confidence 34489999988888665444 449999984
No 51
>COG4869 PduL Propanediol utilization protein [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=24.36 E-value=23 Score=31.73 Aligned_cols=32 Identities=31% Similarity=0.381 Sum_probs=27.1
Q ss_pred ccccccccccccccchhhcccCcccHHHHHHH
Q 026843 190 RKLCFKDFALSLSSNSALKQVFPRDVEEAAIL 221 (232)
Q Consensus 190 ~~l~f~~~~~s~s~~~a~~~~f~~d~~eaA~L 221 (232)
+.|.|+|+.++.|...|+.--...||+.||.+
T Consensus 168 R~Lifd~v~iRv~~df~~emHiDtDEANAa~~ 199 (210)
T COG4869 168 RPLIFDDVVIRVSPDFALEMHIDTDEANAAGF 199 (210)
T ss_pred cceeeeeEEEEEccccceeeecccchhccccc
Confidence 67889999999998877777778899999864
No 52
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=23.59 E-value=32 Score=34.58 Aligned_cols=34 Identities=26% Similarity=0.490 Sum_probs=23.1
Q ss_pred CCCCccccCCCCCC-CCcccCCCCCCc----------ccchHHHH
Q 026843 89 NNTVRICSDCNTTT-TPLWRSGPRGPK----------SLCNACGI 122 (232)
Q Consensus 89 ~~~~~~C~~Cgtt~-TP~WRrGP~G~~----------~LCNACGL 122 (232)
+-..+.|.+||... +++=+-+|++.. +.||+||-
T Consensus 158 WvN~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~ 202 (500)
T KOG0909|consen 158 WVNNPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGT 202 (500)
T ss_pred ecCCCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCC
Confidence 34567899999876 555444444322 68999996
No 53
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=23.16 E-value=14 Score=24.60 Aligned_cols=32 Identities=28% Similarity=0.682 Sum_probs=18.9
Q ss_pred cccCCCCCCCCcc----cCCCCCCc--ccchHHHHHHH
Q 026843 94 ICSDCNTTTTPLW----RSGPRGPK--SLCNACGIRQR 125 (232)
Q Consensus 94 ~C~~Cgtt~TP~W----RrGP~G~~--~LCNACGL~~~ 125 (232)
.|..|+-.+.-.| |++.++.. ..|..||-+|+
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeC
Confidence 4777876654333 55555532 36777876553
No 54
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=22.81 E-value=21 Score=26.92 Aligned_cols=36 Identities=19% Similarity=0.427 Sum_probs=27.8
Q ss_pred CccccCCCCCCCCcccCCCCCCcccchHHHHHHHHh
Q 026843 92 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKA 127 (232)
Q Consensus 92 ~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~k~ 127 (232)
.-.|-.|.+..|-.|.+..+....=|-+||......
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~ 43 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQP 43 (71)
T ss_pred CccCCCCcCccEEEEEEeCCceEEEecCCCCeeccC
Confidence 457999999999887665556678999999866543
No 55
>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=22.74 E-value=30 Score=23.35 Aligned_cols=29 Identities=21% Similarity=0.535 Sum_probs=19.0
Q ss_pred ccccCCCCCCCCcccCCCCCCcccchHHHH
Q 026843 93 RICSDCNTTTTPLWRSGPRGPKSLCNACGI 122 (232)
Q Consensus 93 ~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL 122 (232)
-.|.+|+..-+ .|+.-.+.....|-.||-
T Consensus 6 y~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFE-VLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeE-EEEecCCCCCCCCCCCCC
Confidence 36888887555 565433344567988886
No 56
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.12 E-value=36 Score=29.49 Aligned_cols=33 Identities=24% Similarity=0.495 Sum_probs=24.3
Q ss_pred CCCCccccCCCCCCCCcccCCCCCCcccchHHHHHHHHhhhH
Q 026843 89 NNTVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARKA 130 (232)
Q Consensus 89 ~~~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~k~r~~ 130 (232)
......|..||. ..+....|..||..+..-..+
T Consensus 306 ~~tS~~C~~cg~---------~~~r~~~C~~cg~~~~rD~na 338 (364)
T COG0675 306 YYTSKTCPCCGH---------LSGRLFKCPRCGFVHDRDVNA 338 (364)
T ss_pred CCCcccccccCC---------ccceeEECCCCCCeehhhHHH
Confidence 456788999999 445567999999876554443
No 57
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=21.60 E-value=35 Score=23.36 Aligned_cols=30 Identities=23% Similarity=0.495 Sum_probs=20.7
Q ss_pred ccccCCCCCCCCcccCCCCCCcccchHHHHHHHHh
Q 026843 93 RICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKA 127 (232)
Q Consensus 93 ~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~~k~ 127 (232)
-.|.+||...+.. .+...-|..||-+.-.+
T Consensus 3 Y~C~~Cg~~~~~~-----~~~~irC~~CG~rIlyK 32 (44)
T smart00659 3 YICGECGRENEIK-----SKDVVRCRECGYRILYK 32 (44)
T ss_pred EECCCCCCEeecC-----CCCceECCCCCceEEEE
Confidence 3699999977654 22356899999765433
No 58
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=21.50 E-value=30 Score=29.67 Aligned_cols=34 Identities=24% Similarity=0.439 Sum_probs=26.2
Q ss_pred CCCccccCCCCCCCCcccCCCCCCcccchHHHHHH
Q 026843 90 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQ 124 (232)
Q Consensus 90 ~~~~~C~~Cgtt~TP~WRrGP~G~~~LCNACGL~~ 124 (232)
..-..|.-|+...|++-+.+-.- -.-|.|||-..
T Consensus 103 ~~yv~C~~c~s~dt~l~~~~R~~-~l~c~acGa~~ 136 (151)
T COG1601 103 AEYVKCKECGSPDTELIKEERLL-FLKCEACGAIR 136 (151)
T ss_pred HheeEeccCCCCchhhhhhhhhH-hhHHHHhCCcc
Confidence 45678999999999999884433 46899998543
No 59
>PF15396 FAM60A: Protein Family FAM60A
Probab=21.36 E-value=52 Score=29.89 Aligned_cols=18 Identities=28% Similarity=0.575 Sum_probs=14.1
Q ss_pred cccchHHHHHHHHhhhHH
Q 026843 114 KSLCNACGIRQRKARKAM 131 (232)
Q Consensus 114 ~~LCNACGL~~~k~r~~~ 131 (232)
..+||||-|.+++-++.+
T Consensus 49 GeICNACVLLVKRwKKLP 66 (213)
T PF15396_consen 49 GEICNACVLLVKRWKKLP 66 (213)
T ss_pred chhhHHHHHHHHHHhhCC
Confidence 359999999888766554
No 60
>PHA02998 RNA polymerase subunit; Provisional
Probab=20.56 E-value=28 Score=31.18 Aligned_cols=36 Identities=19% Similarity=0.457 Sum_probs=27.9
Q ss_pred CCccccCCCCCCCCcc----cCCCCCCc--ccchHHHHHHHH
Q 026843 91 TVRICSDCNTTTTPLW----RSGPRGPK--SLCNACGIRQRK 126 (232)
Q Consensus 91 ~~~~C~~Cgtt~TP~W----RrGP~G~~--~LCNACGL~~~k 126 (232)
....|..|+-..+--| |++.++.. ..|..||-+|+-
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 4578999998886655 77877743 289999998874
No 61
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=20.25 E-value=64 Score=23.88 Aligned_cols=15 Identities=20% Similarity=0.651 Sum_probs=12.5
Q ss_pred cccCCCCCC-CCcccC
Q 026843 94 ICSDCNTTT-TPLWRS 108 (232)
Q Consensus 94 ~C~~Cgtt~-TP~WRr 108 (232)
.|.+|+++. |..|..
T Consensus 17 ~CP~Cgs~~~T~~W~G 32 (61)
T PRK08351 17 RCPVCGSRDLSDEWFD 32 (61)
T ss_pred cCCCCcCCcccccccc
Confidence 599999888 888875
Done!