Query 020996
Match_columns 318
No_of_seqs 161 out of 659
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 06:47:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020996.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020996hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00202 ZnF_GATA Zinc finger D 99.5 1.4E-14 3E-19 106.8 4.4 44 243-289 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.5 2.2E-14 4.7E-19 104.6 3.3 47 240-288 2-48 (52)
3 PF00320 GATA: GATA zinc finge 99.4 2.8E-14 6E-19 97.3 0.2 35 244-278 1-35 (36)
4 KOG1601 GATA-4/5/6 transcripti 99.1 1.4E-10 3.1E-15 96.8 4.5 69 241-309 199-301 (340)
5 COG5641 GAT1 GATA Zn-finger-co 97.9 5.5E-06 1.2E-10 84.1 2.0 53 242-296 159-215 (498)
6 KOG3554 Histone deacetylase co 89.2 0.47 1E-05 49.6 4.4 36 240-275 385-422 (693)
7 COG5641 GAT1 GATA Zn-finger-co 71.0 2.4 5.3E-05 44.0 1.8 38 241-278 297-335 (498)
8 PF14803 Nudix_N_2: Nudix N-te 62.0 1.9 4.2E-05 29.7 -0.6 30 242-271 1-30 (34)
9 PF01783 Ribosomal_L32p: Ribos 51.9 4.8 0.0001 30.0 -0.0 27 239-275 24-50 (56)
10 PLN03119 putative ADP-ribosyla 51.8 5.3 0.00012 42.7 0.3 33 238-272 20-52 (648)
11 COG2816 NPY1 NTP pyrophosphohy 51.2 6.1 0.00013 38.5 0.6 31 240-274 110-140 (279)
12 KOG3740 Uncharacterized conser 46.5 11 0.00024 40.7 1.7 37 238-274 459-498 (706)
13 PRK03988 translation initiatio 46.2 5.6 0.00012 34.8 -0.5 32 241-273 102-133 (138)
14 TIGR00311 aIF-2beta translatio 44.3 6.5 0.00014 34.2 -0.4 31 242-273 98-128 (133)
15 PF01412 ArfGap: Putative GTPa 43.8 14 0.00031 30.5 1.6 36 238-275 10-45 (116)
16 PLN03131 hypothetical protein; 43.2 9 0.00019 41.4 0.4 33 238-272 20-52 (705)
17 COG5347 GTPase-activating prot 42.8 9.5 0.00021 37.6 0.5 33 239-273 18-50 (319)
18 TIGR01385 TFSII transcription 41.8 10 0.00022 36.9 0.4 36 238-274 255-297 (299)
19 smart00653 eIF2B_5 domain pres 40.7 7.7 0.00017 32.7 -0.4 30 241-271 80-109 (110)
20 PF04810 zf-Sec23_Sec24: Sec23 40.6 9.6 0.00021 26.5 0.1 32 241-272 2-33 (40)
21 PRK12336 translation initiatio 38.0 8.9 0.00019 35.0 -0.5 34 241-275 98-131 (201)
22 PF12760 Zn_Tnp_IS1595: Transp 37.5 13 0.00029 26.2 0.4 30 239-271 16-45 (46)
23 smart00105 ArfGap Putative GTP 37.4 20 0.00043 29.5 1.5 34 240-275 2-35 (112)
24 PF08271 TF_Zn_Ribbon: TFIIB z 35.4 10 0.00022 26.4 -0.4 32 243-277 2-33 (43)
25 KOG1598 Transcription initiati 35.3 19 0.00041 38.0 1.3 49 242-293 1-51 (521)
26 PF07282 OrfB_Zn_ribbon: Putat 35.1 12 0.00026 27.7 -0.1 31 240-274 27-57 (69)
27 PF02701 zf-Dof: Dof domain, z 34.9 50 0.0011 26.2 3.2 43 240-282 4-49 (63)
28 PLN03114 ADP-ribosylation fact 33.1 23 0.00051 36.2 1.5 35 239-275 20-54 (395)
29 PF09297 zf-NADH-PPase: NADH p 31.7 8.4 0.00018 25.4 -1.3 29 241-273 3-31 (32)
30 COG5349 Uncharacterized protei 31.0 24 0.00053 31.1 1.1 36 239-277 19-54 (126)
31 PF01096 TFIIS_C: Transcriptio 30.6 7.4 0.00016 27.0 -1.7 32 243-274 2-39 (39)
32 PRK12286 rpmF 50S ribosomal pr 29.7 24 0.00051 26.8 0.7 26 238-272 24-49 (57)
33 PF01873 eIF-5_eIF-2B: Domain 29.1 15 0.00031 31.7 -0.6 29 242-271 94-122 (125)
34 TIGR01031 rpmF_bact ribosomal 28.8 16 0.00035 27.4 -0.3 23 239-270 24-46 (55)
35 PF11781 RRN7: RNA polymerase 27.4 24 0.00053 24.5 0.4 26 241-271 8-33 (36)
36 PRK00085 recO DNA repair prote 26.9 26 0.00056 31.4 0.6 35 235-270 143-177 (247)
37 PF15396 FAM60A: Protein Famil 26.2 31 0.00067 32.8 0.9 18 263-280 49-66 (213)
38 PRK00241 nudC NADH pyrophospha 25.8 22 0.00048 33.4 -0.1 31 240-274 98-128 (256)
39 PF12773 DZR: Double zinc ribb 25.0 32 0.00069 24.0 0.6 30 240-274 11-40 (50)
40 COG3952 Predicted membrane pro 24.5 22 0.00048 30.8 -0.3 19 255-275 77-95 (113)
41 PF13248 zf-ribbon_3: zinc-rib 23.5 48 0.001 21.1 1.2 23 242-272 3-25 (26)
42 TIGR00244 transcriptional regu 22.4 42 0.00091 30.2 1.0 33 243-275 2-40 (147)
43 smart00778 Prim_Zn_Ribbon Zinc 22.1 48 0.001 23.4 1.0 29 242-271 4-33 (37)
44 KOG0909 Peptide:N-glycanase [P 21.2 37 0.00081 35.6 0.5 33 241-273 161-204 (500)
45 PRK00423 tfb transcription ini 20.7 47 0.001 31.8 1.0 12 263-274 30-41 (310)
46 KOG0703 Predicted GTPase-activ 20.6 35 0.00077 33.5 0.2 31 238-270 22-52 (287)
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=99.51 E-value=1.4e-14 Score=106.77 Aligned_cols=44 Identities=45% Similarity=0.927 Sum_probs=38.5
Q ss_pred ccCCCCCCCCCCcCCCCCCChhhhhhhhhhhhhCCCCCCCCCCCCCC
Q 020996 243 RCSHCLSQRTPQWRAGPLGPKTLCNACGVRYKSGRLLPEYRPAKSPT 289 (318)
Q Consensus 243 ~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLrykkgrllP~yrPa~sP~ 289 (318)
.|+||++++||+||+||.|..+|||||||||++++ ..||...+.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~---~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG---VMRPLSKRK 44 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC---CCCCcccCc
Confidence 59999999999999999998999999999999977 456665554
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.47 E-value=2.2e-14 Score=104.64 Aligned_cols=47 Identities=53% Similarity=0.992 Sum_probs=39.7
Q ss_pred CCcccCCCCCCCCCCcCCCCCCChhhhhhhhhhhhhCCCCCCCCCCCCC
Q 020996 240 QGRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRYKSGRLLPEYRPAKSP 288 (318)
Q Consensus 240 ~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLrykkgrllP~yrPa~sP 288 (318)
..+.|.||++++||+||+||.|..+|||||||+|++++.+ +||....
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~--~rp~~~~ 48 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL--KRPLSLK 48 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC--CCccccc
Confidence 4578999999999999999999889999999999997654 3444433
No 3
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.41 E-value=2.8e-14 Score=97.26 Aligned_cols=35 Identities=57% Similarity=1.150 Sum_probs=28.3
Q ss_pred cCCCCCCCCCCcCCCCCCChhhhhhhhhhhhhCCC
Q 020996 244 CSHCLSQRTPQWRAGPLGPKTLCNACGVRYKSGRL 278 (318)
Q Consensus 244 Cs~Cgtt~TP~WRrGP~G~ktLCNACGLrykkgrl 278 (318)
|.||++++||+||+||.|..+||||||++|++++.
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 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=99.06 E-value=1.4e-10 Score=96.80 Aligned_cols=69 Identities=61% Similarity=1.103 Sum_probs=57.4
Q ss_pred CcccCCCCCCCCCCcCCCCCCChhhhhhhhhhhhhC---CCCCCCCCCCCCC--------------cccccccc------
Q 020996 241 GRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRYKSG---RLLPEYRPAKSPT--------------FVSYLHSN------ 297 (318)
Q Consensus 241 ~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLrykkg---rllP~yrPa~sP~--------------f~~~~HSn------ 297 (318)
...|.+|+++.||+||+|+.|...+|||||++|+++ +.++.++....+. +....|.+
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPRNVSPKGSGAVKGRTFTKSLHSNSAQLLL 278 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCccccccccCccccccccCCCccccccCCCCCcccccchhhhhh
Confidence 588999999999999999999999999999999998 6778888776666 55566666
Q ss_pred -----------cchHHHHHHHhc
Q 020996 298 -----------SHKKVLEMRMAL 309 (318)
Q Consensus 298 -----------shkkV~~~r~~~ 309 (318)
.+.+++++++.-
T Consensus 279 ~~~~~~~~~~~~~~~~~~~~r~~ 301 (340)
T KOG1601|consen 279 APSKSEPPLLSSHQRVAEVRRYR 301 (340)
T ss_pred hhcccCccccccchHHHHHhhcc
Confidence 677777776643
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=97.87 E-value=5.5e-06 Score=84.11 Aligned_cols=53 Identities=30% Similarity=0.497 Sum_probs=42.8
Q ss_pred cccCCCCCCCCCCcCCCCCC----ChhhhhhhhhhhhhCCCCCCCCCCCCCCccccccc
Q 020996 242 RRCSHCLSQRTPQWRAGPLG----PKTLCNACGVRYKSGRLLPEYRPAKSPTFVSYLHS 296 (318)
Q Consensus 242 r~Cs~Cgtt~TP~WRrGP~G----~ktLCNACGLrykkgrllP~yrPa~sP~f~~~~HS 296 (318)
..|.+|.++.||+|||+..+ .-+|||||||+|+-++...+ |...+..+...|.
T Consensus 159 ~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~--P~t~ks~~~ks~~ 215 (498)
T COG5641 159 HVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRA--PISLKSDSIKSRS 215 (498)
T ss_pred chhccccccCCccccccccccccCCccccccccccccccCCcCC--Ccccccccccccc
Confidence 38999999999999999993 38999999999997665432 7777766666555
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=89.24 E-value=0.47 Score=49.57 Aligned_cols=36 Identities=31% Similarity=0.754 Sum_probs=30.6
Q ss_pred CCcccCCCCCCCCCCc--CCCCCCChhhhhhhhhhhhh
Q 020996 240 QGRRCSHCLSQRTPQW--RAGPLGPKTLCNACGVRYKS 275 (318)
Q Consensus 240 ~~r~Cs~Cgtt~TP~W--RrGP~G~ktLCNACGLrykk 275 (318)
.++.|.+|+++..-+| .-+|.-...||-.|-++|+|
T Consensus 385 ~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKK 422 (693)
T KOG3554|consen 385 DGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKK 422 (693)
T ss_pred CCCcccccccccccceeccCCCCccchhhHHHHHHHHH
Confidence 3789999999999999 44555556799999999998
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=71.00 E-value=2.4 Score=44.01 Aligned_cols=38 Identities=26% Similarity=0.371 Sum_probs=31.4
Q ss_pred CcccCCCCC-CCCCCcCCCCCCChhhhhhhhhhhhhCCC
Q 020996 241 GRRCSHCLS-QRTPQWRAGPLGPKTLCNACGVRYKSGRL 278 (318)
Q Consensus 241 ~r~Cs~Cgt-t~TP~WRrGP~G~ktLCNACGLrykkgrl 278 (318)
..-|.+|++ +.||.||+...-..++|||||+..+..+.
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~~ 335 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPGS 335 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCCccc
Confidence 556777776 78999999888778999999999987554
No 8
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=61.99 E-value=1.9 Score=29.73 Aligned_cols=30 Identities=23% Similarity=0.560 Sum_probs=15.2
Q ss_pred cccCCCCCCCCCCcCCCCCCChhhhhhhhh
Q 020996 242 RRCSHCLSQRTPQWRAGPLGPKTLCNACGV 271 (318)
Q Consensus 242 r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGL 271 (318)
+.|.+||..-+-.=-.|.+-.+.+|.+||-
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 469999987543333555556789999984
No 9
>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=51.91 E-value=4.8 Score=29.96 Aligned_cols=27 Identities=30% Similarity=0.834 Sum_probs=19.4
Q ss_pred CCCcccCCCCCCCCCCcCCCCCCChhhhhhhhhhhhh
Q 020996 239 QQGRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRYKS 275 (318)
Q Consensus 239 ~~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLrykk 275 (318)
.....|.+||...-| ..+|.+|| +|+.
T Consensus 24 ~~l~~c~~cg~~~~~---------H~vc~~cG-~y~~ 50 (56)
T PF01783_consen 24 PNLVKCPNCGEPKLP---------HRVCPSCG-YYKG 50 (56)
T ss_dssp TSEEESSSSSSEEST---------TSBCTTTB-BSSS
T ss_pred cceeeeccCCCEecc---------cEeeCCCC-eECC
Confidence 456789999964432 68999999 4443
No 10
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=51.79 E-value=5.3 Score=42.71 Aligned_cols=33 Identities=30% Similarity=0.549 Sum_probs=27.3
Q ss_pred cCCCcccCCCCCCCCCCcCCCCCCChhhhhhhhhh
Q 020996 238 QQQGRRCSHCLSQRTPQWRAGPLGPKTLCNACGVR 272 (318)
Q Consensus 238 ~~~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLr 272 (318)
.+..+.|++|+... |.|=.=..| -.+|-.|.=.
T Consensus 20 lPgNk~CADCgs~~-P~WASiNlG-IFICi~CSGI 52 (648)
T PLN03119 20 LPPNRRCINCNSLG-PQYVCTTFW-TFVCMACSGI 52 (648)
T ss_pred CcCCCccccCCCCC-CCceeeccc-eEEeccchhh
Confidence 46779999999866 999888888 7899999643
No 11
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=51.18 E-value=6.1 Score=38.50 Aligned_cols=31 Identities=29% Similarity=0.567 Sum_probs=24.8
Q ss_pred CCcccCCCCCCCCCCcCCCCCCChhhhhhhhhhhh
Q 020996 240 QGRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRYK 274 (318)
Q Consensus 240 ~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLryk 274 (318)
..+.|.+||+...+ +. .|.+.+|+.||.++-
T Consensus 110 ~~RFCg~CG~~~~~--~~--~g~~~~C~~cg~~~f 140 (279)
T COG2816 110 SHRFCGRCGTKTYP--RE--GGWARVCPKCGHEHF 140 (279)
T ss_pred hCcCCCCCCCcCcc--cc--CceeeeCCCCCCccC
Confidence 45899999998887 34 466789999998764
No 12
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.51 E-value=11 Score=40.70 Aligned_cols=37 Identities=19% Similarity=0.568 Sum_probs=29.9
Q ss_pred cCCCcccCCCCCCCCCCcCCCCCC---Chhhhhhhhhhhh
Q 020996 238 QQQGRRCSHCLSQRTPQWRAGPLG---PKTLCNACGVRYK 274 (318)
Q Consensus 238 ~~~~r~Cs~Cgtt~TP~WRrGP~G---~ktLCNACGLryk 274 (318)
..+...|..|.+.-||.|+.-+.| ...+|.+|----.
T Consensus 459 a~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSnq 498 (706)
T KOG3740|consen 459 ATEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSNQ 498 (706)
T ss_pred cCCchhhhhcccccccccccccccCcchHHHHHhhhhhcc
Confidence 345788999999999999987776 4689999976443
No 13
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=46.23 E-value=5.6 Score=34.79 Aligned_cols=32 Identities=28% Similarity=0.381 Sum_probs=23.5
Q ss_pred CcccCCCCCCCCCCcCCCCCCChhhhhhhhhhh
Q 020996 241 GRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRY 273 (318)
Q Consensus 241 ~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLry 273 (318)
--.|..|+..+|-.=+++- ---.-|+|||-..
T Consensus 102 yVlC~~C~spdT~l~k~~r-~~~l~C~ACGa~~ 133 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGR-IWVLKCEACGAET 133 (138)
T ss_pred cEECCCCCCCCcEEEEcCC-eEEEEcccCCCCC
Confidence 3579999999998877532 1135899999653
No 14
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=44.31 E-value=6.5 Score=34.21 Aligned_cols=31 Identities=26% Similarity=0.501 Sum_probs=23.0
Q ss_pred cccCCCCCCCCCCcCCCCCCChhhhhhhhhhh
Q 020996 242 RRCSHCLSQRTPQWRAGPLGPKTLCNACGVRY 273 (318)
Q Consensus 242 r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLry 273 (318)
-.|..|+..+|-.=+++- ---.-|+|||-..
T Consensus 98 VlC~~C~sPdT~l~k~~r-~~~l~C~ACGa~~ 128 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGR-VSLLKCEACGAKA 128 (133)
T ss_pred EECCCCCCCCcEEEEeCC-eEEEecccCCCCC
Confidence 579999999998877532 1134899999653
No 15
>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=43.85 E-value=14 Score=30.45 Aligned_cols=36 Identities=25% Similarity=0.588 Sum_probs=25.2
Q ss_pred cCCCcccCCCCCCCCCCcCCCCCCChhhhhhhhhhhhh
Q 020996 238 QQQGRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRYKS 275 (318)
Q Consensus 238 ~~~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLrykk 275 (318)
.+..+.|++|+... |.|-.=..| -.||-.|.-..+.
T Consensus 10 ~~~N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~ 45 (116)
T PF01412_consen 10 KPGNKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRS 45 (116)
T ss_dssp STTCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHH
T ss_pred CcCcCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHH
Confidence 35679999999554 599988889 8999999977765
No 16
>PLN03131 hypothetical protein; Provisional
Probab=43.23 E-value=9 Score=41.42 Aligned_cols=33 Identities=27% Similarity=0.526 Sum_probs=27.1
Q ss_pred cCCCcccCCCCCCCCCCcCCCCCCChhhhhhhhhh
Q 020996 238 QQQGRRCSHCLSQRTPQWRAGPLGPKTLCNACGVR 272 (318)
Q Consensus 238 ~~~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLr 272 (318)
.+..++|++|+... |.|-.=..| ..+|-.|.=.
T Consensus 20 ~PgNk~CADCga~~-P~WASiNlG-IFICi~CSGI 52 (705)
T PLN03131 20 LPPNRRCINCNSLG-PQFVCTNFW-TFICMTCSGI 52 (705)
T ss_pred CcCCCccccCCCCC-CCeeEeccc-eEEchhchhh
Confidence 46779999999754 999888888 8899999644
No 17
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=42.84 E-value=9.5 Score=37.58 Aligned_cols=33 Identities=27% Similarity=0.699 Sum_probs=28.8
Q ss_pred CCCcccCCCCCCCCCCcCCCCCCChhhhhhhhhhh
Q 020996 239 QQGRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRY 273 (318)
Q Consensus 239 ~~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLry 273 (318)
+....|+.|+... |+|=.=..| -.||=-|.=-.
T Consensus 18 ~~Nk~CaDCga~~-P~W~S~nlG-vfiCi~CagvH 50 (319)
T COG5347 18 SSNKKCADCGAPN-PTWASVNLG-VFLCIDCAGVH 50 (319)
T ss_pred cccCccccCCCCC-CceEecccC-eEEEeecchhh
Confidence 4678999999999 999999999 89999996433
No 18
>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=41.78 E-value=10 Score=36.95 Aligned_cols=36 Identities=25% Similarity=0.567 Sum_probs=26.0
Q ss_pred cCCCcccCCCCCCCCCCc----CCCCCCChh---hhhhhhhhhh
Q 020996 238 QQQGRRCSHCLSQRTPQW----RAGPLGPKT---LCNACGVRYK 274 (318)
Q Consensus 238 ~~~~r~Cs~Cgtt~TP~W----RrGP~G~kt---LCNACGLryk 274 (318)
......|..|+-...-.| |.+.++ -+ .|..||-+|+
T Consensus 255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEp-mT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 255 VTDLFTCGKCKQKKCTYYQLQTRSADEP-MTTFVTCEECGNRWK 297 (299)
T ss_pred CcccccCCCCCCccceEEEecccCCCCC-CeEEEEcCCCCCeee
Confidence 344689999998777655 444444 33 8999999886
No 19
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=40.71 E-value=7.7 Score=32.70 Aligned_cols=30 Identities=27% Similarity=0.355 Sum_probs=22.2
Q ss_pred CcccCCCCCCCCCCcCCCCCCChhhhhhhhh
Q 020996 241 GRRCSHCLSQRTPQWRAGPLGPKTLCNACGV 271 (318)
Q Consensus 241 ~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGL 271 (318)
--.|..|+..+|-+=+.+- ---.-|+|||-
T Consensus 80 yVlC~~C~spdT~l~k~~r-~~~l~C~aCGa 109 (110)
T smart00653 80 YVLCPECGSPDTELIKENR-LFFLKCEACGA 109 (110)
T ss_pred cEECCCCCCCCcEEEEeCC-eEEEEccccCC
Confidence 3579999999998887731 11346999995
No 20
>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=40.57 E-value=9.6 Score=26.51 Aligned_cols=32 Identities=28% Similarity=0.598 Sum_probs=21.5
Q ss_pred CcccCCCCCCCCCCcCCCCCCChhhhhhhhhh
Q 020996 241 GRRCSHCLSQRTPQWRAGPLGPKTLCNACGVR 272 (318)
Q Consensus 241 ~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLr 272 (318)
+.+|.+|++---|.-+-...|....||-||..
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 46899999998888888888888899999974
No 21
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=37.98 E-value=8.9 Score=34.99 Aligned_cols=34 Identities=24% Similarity=0.301 Sum_probs=25.0
Q ss_pred CcccCCCCCCCCCCcCCCCCCChhhhhhhhhhhhh
Q 020996 241 GRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRYKS 275 (318)
Q Consensus 241 ~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLrykk 275 (318)
--.|..|+..+|-+=+.+- ---.-|+|||-..--
T Consensus 98 yV~C~~C~~pdT~l~k~~~-~~~l~C~aCGa~~~v 131 (201)
T PRK12336 98 YVICSECGLPDTRLVKEDR-VLMLRCDACGAHRPV 131 (201)
T ss_pred eEECCCCCCCCcEEEEcCC-eEEEEcccCCCCccc
Confidence 3579999999998877631 113479999987643
No 22
>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=37.50 E-value=13 Score=26.22 Aligned_cols=30 Identities=30% Similarity=0.532 Sum_probs=21.7
Q ss_pred CCCcccCCCCCCCCCCcCCCCCCChhhhhhhhh
Q 020996 239 QQGRRCSHCLSQRTPQWRAGPLGPKTLCNACGV 271 (318)
Q Consensus 239 ~~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGL 271 (318)
+.+..|.+||.+ ...|.++ .+ ..-|++|+-
T Consensus 16 ~~g~~CP~Cg~~-~~~~~~~-~~-~~~C~~C~~ 45 (46)
T PF12760_consen 16 PDGFVCPHCGST-KHYRLKT-RG-RYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCCe-eeEEeCC-CC-eEECCCCCC
Confidence 345779999998 5555555 34 789999974
No 23
>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=37.37 E-value=20 Score=29.51 Aligned_cols=34 Identities=29% Similarity=0.668 Sum_probs=28.5
Q ss_pred CCcccCCCCCCCCCCcCCCCCCChhhhhhhhhhhhh
Q 020996 240 QGRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRYKS 275 (318)
Q Consensus 240 ~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLrykk 275 (318)
....|++|+. .-|.|=.=..| -.||-.|.-.-+.
T Consensus 2 ~N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~ 35 (112)
T smart00105 2 GNKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRS 35 (112)
T ss_pred CCCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHh
Confidence 4688999998 55999888888 8999999877665
No 24
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=35.40 E-value=10 Score=26.37 Aligned_cols=32 Identities=22% Similarity=0.603 Sum_probs=19.3
Q ss_pred ccCCCCCCCCCCcCCCCCCChhhhhhhhhhhhhCC
Q 020996 243 RCSHCLSQRTPQWRAGPLGPKTLCNACGVRYKSGR 277 (318)
Q Consensus 243 ~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLrykkgr 277 (318)
.|.+|+.+. -.+- --.| ..+|..||+-+.-.-
T Consensus 2 ~Cp~Cg~~~-~~~D-~~~g-~~vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 2 KCPNCGSKE-IVFD-PERG-ELVCPNCGLVLEENI 33 (43)
T ss_dssp SBTTTSSSE-EEEE-TTTT-EEEETTT-BBEE-TT
T ss_pred CCcCCcCCc-eEEc-CCCC-eEECCCCCCEeeccc
Confidence 588898866 2222 2234 679999998766543
No 25
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=35.30 E-value=19 Score=37.97 Aligned_cols=49 Identities=20% Similarity=0.469 Sum_probs=29.7
Q ss_pred cccCCCCCCCCCCcCCCCCCChhhhhhhhhhhhhCCCCC--CCCCCCCCCcccc
Q 020996 242 RRCSHCLSQRTPQWRAGPLGPKTLCNACGVRYKSGRLLP--EYRPAKSPTFVSY 293 (318)
Q Consensus 242 r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLrykkgrllP--~yrPa~sP~f~~~ 293 (318)
..|.|||.+.-- |+--.| ...|+|||.-.......- .+-...+.+|++.
T Consensus 1 ~~C~~C~~s~fe--~d~a~g-~~~C~~CG~v~E~~~ivsev~F~e~~~G~~v~~ 51 (521)
T KOG1598|consen 1 MVCKNCGGSNFE--RDEATG-NLYCTACGTVLEYNNIVAEVTFVEGAQGQFVRV 51 (521)
T ss_pred CcCCCCCCCCcc--cccccC-CceeccccceeeccceeEEeeeecccceeEEec
Confidence 369999987643 344456 789999998765433321 1112256666653
No 26
>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=35.14 E-value=12 Score=27.72 Aligned_cols=31 Identities=19% Similarity=0.518 Sum_probs=23.5
Q ss_pred CCcccCCCCCCCCCCcCCCCCCChhhhhhhhhhhh
Q 020996 240 QGRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRYK 274 (318)
Q Consensus 240 ~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLryk 274 (318)
-...|..||....- ...+....|..||..+-
T Consensus 27 TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK----RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCccCccccccc----ccccceEEcCCCCCEEC
Confidence 46889999986654 44566789999998753
No 27
>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=34.90 E-value=50 Score=26.20 Aligned_cols=43 Identities=23% Similarity=0.417 Sum_probs=32.0
Q ss_pred CCcccCCCCCCCCCCc---CCCCCCChhhhhhhhhhhhhCCCCCCC
Q 020996 240 QGRRCSHCLSQRTPQW---RAGPLGPKTLCNACGVRYKSGRLLPEY 282 (318)
Q Consensus 240 ~~r~Cs~Cgtt~TP~W---RrGP~G~ktLCNACGLrykkgrllP~y 282 (318)
+...|..|..+.|--= --...-+...|-+|..+|..|+.|...
T Consensus 4 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnV 49 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNV 49 (63)
T ss_pred cCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCC
Confidence 5678999999888533 122334578999999999999877544
No 28
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=33.12 E-value=23 Score=36.18 Aligned_cols=35 Identities=26% Similarity=0.655 Sum_probs=28.7
Q ss_pred CCCcccCCCCCCCCCCcCCCCCCChhhhhhhhhhhhh
Q 020996 239 QQGRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRYKS 275 (318)
Q Consensus 239 ~~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLrykk 275 (318)
+..+.|..|+... |.|=.=..| ..||-.|.=.-+.
T Consensus 20 PgNk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRs 54 (395)
T PLN03114 20 SDNKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRS 54 (395)
T ss_pred cCCCcCccCCCCC-CCceeeccc-eeehhhhhHhhcc
Confidence 5678999999864 999998899 8999999655443
No 29
>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=31.74 E-value=8.4 Score=25.39 Aligned_cols=29 Identities=31% Similarity=0.643 Sum_probs=16.7
Q ss_pred CcccCCCCCCCCCCcCCCCCCChhhhhhhhhhh
Q 020996 241 GRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRY 273 (318)
Q Consensus 241 ~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLry 273 (318)
.+.|..||....+. +.|....|.+||..+
T Consensus 3 ~rfC~~CG~~t~~~----~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA----PGGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--BEEE-----SSSS-EEESSSS-EE
T ss_pred CcccCcCCccccCC----CCcCEeECCCCcCEe
Confidence 47899999876543 346678999999753
No 30
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.98 E-value=24 Score=31.10 Aligned_cols=36 Identities=31% Similarity=0.539 Sum_probs=24.4
Q ss_pred CCCcccCCCCCCCCCCcCCCCCCChhhhhhhhhhhhhCC
Q 020996 239 QQGRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRYKSGR 277 (318)
Q Consensus 239 ~~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLrykkgr 277 (318)
+...+|-+||.-.- =+|-.-...-|.|||+.|-..+
T Consensus 19 Gl~grCP~CGeGrL---F~gFLK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 19 GLRGRCPRCGEGRL---FRGFLKVVPACEACGLDYGFAD 54 (126)
T ss_pred HhcCCCCCCCCchh---hhhhcccCchhhhccccccCCc
Confidence 34578999996432 2333444578999999997643
No 31
>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=30.65 E-value=7.4 Score=27.04 Aligned_cols=32 Identities=22% Similarity=0.613 Sum_probs=19.6
Q ss_pred ccCCCCCCCCCCc----CCCCCCCh--hhhhhhhhhhh
Q 020996 243 RCSHCLSQRTPQW----RAGPLGPK--TLCNACGVRYK 274 (318)
Q Consensus 243 ~Cs~Cgtt~TP~W----RrGP~G~k--tLCNACGLryk 274 (318)
.|..||..+.-.| |.++++.. ..|..||-+|+
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 4888888765444 66666632 37999998774
No 32
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=29.74 E-value=24 Score=26.80 Aligned_cols=26 Identities=23% Similarity=0.653 Sum_probs=20.4
Q ss_pred cCCCcccCCCCCCCCCCcCCCCCCChhhhhhhhhh
Q 020996 238 QQQGRRCSHCLSQRTPQWRAGPLGPKTLCNACGVR 272 (318)
Q Consensus 238 ~~~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLr 272 (318)
.+..-.|.+||...-| ..+|..||.|
T Consensus 24 ~~~l~~C~~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 24 APGLVECPNCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred CCcceECCCCCCccCC---------eEECCCCCcC
Confidence 3566789999987765 6799999943
No 33
>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=29.12 E-value=15 Score=31.66 Aligned_cols=29 Identities=34% Similarity=0.571 Sum_probs=22.7
Q ss_pred cccCCCCCCCCCCcCCCCCCChhhhhhhhh
Q 020996 242 RRCSHCLSQRTPQWRAGPLGPKTLCNACGV 271 (318)
Q Consensus 242 r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGL 271 (318)
-.|..|+..+|-+=+++..= -.-|+|||-
T Consensus 94 VlC~~C~spdT~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCC-EEEETTTSC
T ss_pred EEcCCCCCCccEEEEcCCEE-EEEecccCC
Confidence 47999999999888774332 468999995
No 34
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=28.81 E-value=16 Score=27.40 Aligned_cols=23 Identities=26% Similarity=0.728 Sum_probs=18.0
Q ss_pred CCCcccCCCCCCCCCCcCCCCCCChhhhhhhh
Q 020996 239 QQGRRCSHCLSQRTPQWRAGPLGPKTLCNACG 270 (318)
Q Consensus 239 ~~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACG 270 (318)
+..-.|.+||...-| ..+|-.||
T Consensus 24 p~l~~C~~cG~~~~~---------H~vc~~cG 46 (55)
T TIGR01031 24 PTLVVCPNCGEFKLP---------HRVCPSCG 46 (55)
T ss_pred CcceECCCCCCcccC---------eeECCccC
Confidence 556789999985543 67999999
No 35
>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=27.42 E-value=24 Score=24.45 Aligned_cols=26 Identities=31% Similarity=0.714 Sum_probs=19.9
Q ss_pred CcccCCCCCCCCCCcCCCCCCChhhhhhhhh
Q 020996 241 GRRCSHCLSQRTPQWRAGPLGPKTLCNACGV 271 (318)
Q Consensus 241 ~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGL 271 (318)
...|..|+.. |-...+| ...|..||-
T Consensus 8 ~~~C~~C~~~----~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 8 NEPCPVCGSR----WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CCcCCCCCCe----EeEccCC-EEEhhhCce
Confidence 3569999987 5555678 889999984
No 36
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=26.87 E-value=26 Score=31.39 Aligned_cols=35 Identities=17% Similarity=0.413 Sum_probs=28.5
Q ss_pred ccccCCCcccCCCCCCCCCCcCCCCCCChhhhhhhh
Q 020996 235 QQQQQQGRRCSHCLSQRTPQWRAGPLGPKTLCNACG 270 (318)
Q Consensus 235 ~~~~~~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACG 270 (318)
.|-.+....|..||......|-.-.+| +.+|..|+
T Consensus 143 ~G~~p~l~~C~~Cg~~~~~~~f~~~~g-g~~c~~c~ 177 (247)
T PRK00085 143 LGYGLDLDHCAVCGAPGDHRYFSPKEG-GAVCSECG 177 (247)
T ss_pred cCCccchhhHhcCCCCCCceEEecccC-Cccccccc
Confidence 556677889999998877677766677 89999997
No 37
>PF15396 FAM60A: Protein Family FAM60A
Probab=26.15 E-value=31 Score=32.76 Aligned_cols=18 Identities=39% Similarity=0.689 Sum_probs=13.9
Q ss_pred hhhhhhhhhhhhhCCCCC
Q 020996 263 KTLCNACGVRYKSGRLLP 280 (318)
Q Consensus 263 ktLCNACGLrykkgrllP 280 (318)
+.+||||=|.+++-+-||
T Consensus 49 GeICNACVLLVKRwKKLP 66 (213)
T PF15396_consen 49 GEICNACVLLVKRWKKLP 66 (213)
T ss_pred chhhHHHHHHHHHHhhCC
Confidence 369999999998754444
No 38
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=25.84 E-value=22 Score=33.38 Aligned_cols=31 Identities=29% Similarity=0.502 Sum_probs=22.8
Q ss_pred CCcccCCCCCCCCCCcCCCCCCChhhhhhhhhhhh
Q 020996 240 QGRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRYK 274 (318)
Q Consensus 240 ~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLryk 274 (318)
..+.|.+||...... ..|....|.+||..+-
T Consensus 98 ~~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 98 SHRFCGYCGHPMHPS----KTEWAMLCPHCRERYY 128 (256)
T ss_pred cCccccccCCCCeec----CCceeEECCCCCCEEC
Confidence 458999999975542 3566789999996543
No 39
>PF12773 DZR: Double zinc ribbon
Probab=25.00 E-value=32 Score=24.00 Aligned_cols=30 Identities=27% Similarity=0.661 Sum_probs=20.5
Q ss_pred CCcccCCCCCCCCCCcCCCCCCChhhhhhhhhhhh
Q 020996 240 QGRRCSHCLSQRTPQWRAGPLGPKTLCNACGVRYK 274 (318)
Q Consensus 240 ~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLryk 274 (318)
..+.|.+||+.-. ........|..||-.+.
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGAENP 40 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcCCCc
Confidence 4678888888766 33444568888887544
No 40
>COG3952 Predicted membrane protein [Function unknown]
Probab=24.52 E-value=22 Score=30.84 Aligned_cols=19 Identities=32% Similarity=0.424 Sum_probs=13.9
Q ss_pred cCCCCCCChhhhhhhhhhhhh
Q 020996 255 WRAGPLGPKTLCNACGVRYKS 275 (318)
Q Consensus 255 WRrGP~G~ktLCNACGLrykk 275 (318)
||.+|-+ .||+|||+...-
T Consensus 77 ~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 77 RRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HhcchHH--HHHHhhhHHHHH
Confidence 4666655 799999997643
No 41
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=23.54 E-value=48 Score=21.08 Aligned_cols=23 Identities=26% Similarity=0.816 Sum_probs=15.0
Q ss_pred cccCCCCCCCCCCcCCCCCCChhhhhhhhhh
Q 020996 242 RRCSHCLSQRTPQWRAGPLGPKTLCNACGVR 272 (318)
Q Consensus 242 r~Cs~Cgtt~TP~WRrGP~G~ktLCNACGLr 272 (318)
+.|.+||....+ + ...|-.||..
T Consensus 3 ~~Cp~Cg~~~~~-------~-~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDP-------D-AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCc-------c-cccChhhCCC
Confidence 568888885432 2 4578888754
No 42
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=22.41 E-value=42 Score=30.18 Aligned_cols=33 Identities=24% Similarity=0.528 Sum_probs=24.8
Q ss_pred ccCCCCCCCCCCc--CCCCCC----Chhhhhhhhhhhhh
Q 020996 243 RCSHCLSQRTPQW--RAGPLG----PKTLCNACGVRYKS 275 (318)
Q Consensus 243 ~Cs~Cgtt~TP~W--RrGP~G----~ktLCNACGLrykk 275 (318)
.|-.|+...|-.- |...+| +.--|.+||-+|-.
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTT 40 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTT 40 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccce
Confidence 6999998888666 555566 33589999998854
No 43
>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=22.05 E-value=48 Score=23.38 Aligned_cols=29 Identities=21% Similarity=0.587 Sum_probs=20.7
Q ss_pred cccCCCCCCCCCCcCCCC-CCChhhhhhhhh
Q 020996 242 RRCSHCLSQRTPQWRAGP-LGPKTLCNACGV 271 (318)
Q Consensus 242 r~Cs~Cgtt~TP~WRrGP-~G~ktLCNACGL 271 (318)
..|-.|+....=.|..-. .| ...|+.||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G-~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRG-TWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCc-CEEeCCCCC
Confidence 569999988776675422 34 679999973
No 44
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=21.15 E-value=37 Score=35.63 Aligned_cols=33 Identities=21% Similarity=0.458 Sum_probs=22.6
Q ss_pred CcccCCCCCCC-CCCcCCCCCCCh----------hhhhhhhhhh
Q 020996 241 GRRCSHCLSQR-TPQWRAGPLGPK----------TLCNACGVRY 273 (318)
Q Consensus 241 ~r~Cs~Cgtt~-TP~WRrGP~G~k----------tLCNACGLry 273 (318)
...|.+||... +++-+-+|.+.. +.||+||---
T Consensus 161 ~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~ 204 (500)
T KOG0909|consen 161 NPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTET 204 (500)
T ss_pred CCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCcc
Confidence 35699999877 555554555432 6899999643
No 45
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.67 E-value=47 Score=31.84 Aligned_cols=12 Identities=25% Similarity=0.880 Sum_probs=5.8
Q ss_pred hhhhhhhhhhhh
Q 020996 263 KTLCNACGVRYK 274 (318)
Q Consensus 263 ktLCNACGLryk 274 (318)
.++|.-||+-+.
T Consensus 30 e~vC~~CG~Vl~ 41 (310)
T PRK00423 30 EIVCADCGLVIE 41 (310)
T ss_pred eEeecccCCccc
Confidence 445555555443
No 46
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=20.63 E-value=35 Score=33.54 Aligned_cols=31 Identities=26% Similarity=0.789 Sum_probs=26.2
Q ss_pred cCCCcccCCCCCCCCCCcCCCCCCChhhhhhhh
Q 020996 238 QQQGRRCSHCLSQRTPQWRAGPLGPKTLCNACG 270 (318)
Q Consensus 238 ~~~~r~Cs~Cgtt~TP~WRrGP~G~ktLCNACG 270 (318)
.+..+.|+.|++. .|.|-.=-.| ..+|-.|.
T Consensus 22 ~~~N~~CADC~a~-~P~WaSwnlG-vFiC~~C~ 52 (287)
T KOG0703|consen 22 EPDNKVCADCGAK-GPRWASWNLG-VFICLRCA 52 (287)
T ss_pred CcccCcccccCCC-CCCeEEeecC-eEEEeecc
Confidence 4568999999999 9999887788 78998773
Done!