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About 10,000 papers for “Conserved sequence”

Identifying Conserved Sequence Motifs

Sufang Wang, Michael Gribskov · 2025

Cited by 1

Consensus sequence (canonical sequence, consensus motif, conserved sequence box)

The Dictionary of Genomics, Transcriptomics and Proteomics · 2015

Cited by 0

Gene-distant conserved sequence clusters are made up of multiple conserved sequence blocks.

Mukta Kundu (32926), Alexander Kuzin (32925), Tzu-Yang Lin (402625) et al. · Figshare · 2015

Shown, is a D. melanogaster relaxed EvoPrint spanning the first (most 5′) 6,351 bp of the vvl 3′ flanking intergenic region that includes the conserved sequence block (CSB) clusters vvl-37 through vvl-41 (indicated by vertical bars in left margin). CSB clusters are resolved by their flanking less-conserved inter-cluster sequences of 150 or more bp. Capital letters represent bases in the D. melanogaster reference sequence that are conserved in all, or all but one, of the orthologous regions within the D. simulans, D. sechellia, D. erecta, D. yakuba, D. ananassae, D. pseudoobscura, D. persimilis, D. willistoni, D. virilis, D. mojavensis and D. grimshawi genomes. Less or non-conserved DNA is shown as lower case gray letters and the lower-case red-font bases indicate invariant spacer length DNA between CSBs. Colored highlighted conserved sequences within the vvl-38 (blue), vvl-39 (yellow), and vvl-41 (purple) clusters represent repeat elements that are discussed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060137#pone.0060137.s006" target="_blank">Text S1</a>.

Cited by 0Open access

Conserved sequence of protease 1447.

Hossein Tarrahimofrad (9016994), Amir Meimandipour (9016997), Sareh Arjmand (9017000) et al. · Figshare · 2020

(A) Protein sequence alignment of the protease 1147 and several closely related sequences. The over residues in the boxed regions represent the conserved catalytic tetrad. (B) The amino acids involved in the catalytic tetrad of protease 1147 (Glu77 –Cys103 –His104 –Gly105) are marked in red ribbon sticks. The accession number of the sequences are represented.

Cited by 0Open access

Sequence alignment and conserved residues.

Young-Sik Sohn (715070), Seong-Gyu Lee (112227), Kwang-Hoon Lee (85689) et al. · Figshare · 2016

(a) Multiple sequence alignment. Sequences of TON_0340 and its homologues from seven distant organisms are aligned. The red and blue columns indicate the amino acids that are 100% and greater than 80% conserved, respectively. The metal-binding residues in the TON_0340 structure are indicated by asterisks. The secondary structure assignment is shown at the top of the sequence. The accession numbers in the sequence databases are TON_0340 (GI: 212223486), bacterium (GI: 150392380; Amet_4702 of Alkaliphilus metalliredigens QYMF), zebrafish (GI: 115313581), frog (GI: 89272814), chicken (GI: 118092080), rat (GI: 291167745) and human (GI: 31874032; C14orf159). (b) Mapping of the invariant residues on the TON_0340 structure. On the surface of the protein, the invariant residues are shown in green and labeled. The bound Mn2+ ions are shown in spheres.

Cited by 0Open access

Sequence conserved for subcellular localization

Rajesh Nair, Burkhard Rost · Protein Science · 2002

The more proteins diverged in sequence, the more difficult it becomes for bioinformatics to infer similarities of protein function and structure from sequence. The precise thresholds used in automated genome annotations depend on the particular aspect of protein function transferred by homology. Here, we presented the first large-scale analysis of the relation between sequence similarity and identity in subcellular localization. Three results stood out: (1) The subcellular compartment is generally more conserved than what might have been expected given that short sequence motifs like nuclear localization signals can alter the native compartment; (2) the sequence conservation of localization is similar between different compartments; and (3) it is similar to the conservation of structure and enzymatic activity. In particular, we found the transition between the regions of conserved and nonconserved localization to be very sharp, although the thresholds for conservation were less well defined than for structure and enzymatic activity. We found that a simple measure for sequence similarity accounting for pairwise sequence identity and alignment length, the HSSP distance, distinguished accurately between protein pairs of identical and different localizations. In fact, BLAST expectation values outperformed the HSSP distance only for alignments in the subtwilight zone. We succeeded in slightly improving the accuracy of inferring localization through homology by fine tuning the thresholds. Finally, we applied our results to the entire SWISS-PROT database and five entirely sequenced eukaryotes.

Cited by 177Open access

The conserved sequence of COI.

Wanli Liu (384073), Zhuo Duan (460222), Dingcheng Wang (226399) et al. · Figshare · 2024

(a) Characteristic features of the COI based on a phylogenetic tree and COI genes show conserved features, including (b) conserved motifs present in the amino acids. (c) The Secondary Structure of COI based on free energy minimization. (d) The 3D of COI protein. (TIF)

Cited by 0Open access

Conserved sequence motifs are not spatially conserved in tertiary structure.

Nermin Celik (142618), Chaille T. Webb (142619), Denisse L. Leyton (142620) et al. · Figshare · 2012

(A) MEME was used to identify six common motifs in the barrel-domains of the 47 autotransporter sequences in the starting set (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043245#s4" target="_blank">Methods</a>). The six motifs were mapped onto the barrel-domain region of the five autotransporters for which crystal structures have been solved: BrkA, EspP, EstA, Hbp and NalP and are indicated by the respective colours. (B) In 1038 sequences, motif number 5 (the β-motif) was confined to the last β-strand and the final residue in the motif was always a bulky hydrophobic residue. In some of these sequences, a second occurrence, or even a third occurrence of the β-motif was detected in strands other than the terminal strand (paler yellow). In 473 sequences the β-motif is found internally within the barrel-domain. In 12 sequences a short “α-tail” segment succeeds the β-motif of the barrel. Given the topology of bacterial β-barrel proteins, the α-helical tail would presumably be positioned within the periplasmic space. (C) Sequences corresponding to the passenger-and α−linker-domains of autotransporters were defined (Methods) and subject to motif analysis using MEME. A single motif corresponding to the α−linker-domains of 31 of the 47 autotransporter sequences in the starting set (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043245#s4" target="_blank">Methods</a>), including EspP, EstA and Hbp was identified and is indicated by blue shading on the crystal structure representations of these proteins. Note, that in the crystallized form of BrkA the corresponding segment of the protein was not visualized.

Cited by 0Open access

Sequence alignments showing the conserved motifs

Aartjan J.W. Te Velthuis, Tadamoto Isogai · Figshare · 2011

Cited by 0Open access

snoRNA sequence and yeast conserved orthologs.

Mohd Firdaus-Raih (454946), Noor Haza Fazlin Hashim (4811082), Izwan Bharudin (4811118) et al. · Figshare · 2018

(A) comparison of predicted box C/D small nucleolar RNA (snoRNA) and ribosomal biogenesis genes in Drosophila melanogaster, Saccaromyces cerevisiae, Coccomyxa subellipsoidea and Glaciozyma antarctica, (B) comparison of predicted conserved orthologs between G. antarctica, Pseudogymnoascus destructans, Cryptococcus neoformans, Saccaromyces cerevisiae, Chaetomium thermophilum and Myceliophthora thermophila.

Cited by 0Open access

Conserved sequence features of TbAK1-3.

Frank Voncken (101666), Fei Gao (29262), Cath Wadforth (420266) et al. · Figshare · 2015

Sequence alignment of TbAK1-3, T. cruzi TcCLB.507241.30, and representative arginine kinases from insects, crustaceans and molluscs. The N-terminal flagellar targeting signal of TbAK1 and the C-terminal PTS1 signal of TbAK2 are shown in bold face. Key residues involved in the binding of ATP and arginine are indicated on top of the alignment. The phosphagen kinase active site signature sequence is printed white bold face on a black background. The conserved α-helical N-terminal domain and C-terminal α/β saddle domain are boxed. Identical amino acids are represented by a dot and gaps are shown as dashes. See Material and Methods for different organism names and gene accession numbers.

Cited by 0Open access

IhtA sequence is conserved across species.

Jeremiah Tattersall (127135), Geeta Vittal Rao (127140), Justin Runac (127144) et al. · Figshare · 2015

The sequence of ihtA of C. trachomatis serovar D, C. muridarum, C. caviae, and C. pneumoniae compared to C. trachomatis serovar L2. The TSS of serovars L2 and D and C. pneumoniae ihtA (indicated in bold) has been experimentally proven while the TSS of the other Chlamydia is predicted.

Cited by 0Open access

Conserved protein sequence alignment of Dynamins.

Rebecca M. Boumil (244357), Verity A. Letts (244359), Monica C. Roberts (244364) et al. · Figshare · 2015

(A) Conserved protein sequence alignment. The upper diagram shows DNM1 sequence conservation among various species and the location of the fitful mutation within the middle domain of the protein. The first splice region (amino acids 399–444) shows the location of the fitful mutation (*408) and the conservation within mammalian, fly and worm dynamins. Notice that the fly and worm orthologs do not have splice variants in this region. The second alternative splicing region is also shown at the end of the PRD domain. GTPase, GTPase domain; Middle, middle domain; PH, pleckstrin homology domain; GED, GTPase effector domain; PRD, proline rich domain. The bottom diagram depicts the mutually exclusive alternative splicing of the Dnm1a and Dnm1b isoforms. (B) Putative orthologues of mouse Dnm1, Dnm2, Dnm3 and Drp (dynamin related protein – official mouse gene symbol, Dnm1l) from different species. For simplicity, the same generic gene symbol is used for all; for simpler eukaryotes, the symbol Dnm refers to their orthologue(s) most like the mammalian Dnm1, Dnm2 or Dnm3. The known or predicted alternate sequences corresponding to mouse Dnm1 exon 10 are also shown. The underlined amino acid symbols show where mouse Dnm1b differs from Dnm1a. The arrow at the bottom shows the highly conserved alanine residue that is mutated to threonine in the mouse Dnm1Ftfl allele. Residues colored in red show amino acid substitutions with respect to mouse Dnm1; for nematode (C.b. - C. briggsae; C.e. – c.elegans), differences between the two Dnm peptides are shown in blue. Peptide sequences were obtained as follows: mouse Dnm1a: GenBank AAA37318, Dnm1b : GenBank EDL08539; human Dnm1a: GenBank AAA02804, Dnm1b: GenBank AAA02803; nematode <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001046#pgen.1001046-Haug1" target="_blank">[48]</a> GenBank AAB72228; fruit fly (D. melanogaster) EMBL CAA42068. The remaining predicted sequences were obtained from analysis using the USCS Genome Browser and draft genome sequence assemblies from the following respective genome centers: chicken (G. gallus), sea lamprey (P. marinus) and nematode (C. briggsae) - Genome Sequencing Center, Washington University School of Medicine; opposum (M. domestica) and lizard (A. carolinensis), The Broad Institute; xenopus (X. tropicalis), lancelet (B. floridae), and sea squirt (C. intestinalis) - DoE Joint Genome Institute; sea urchin (S. purpuratus) - Baylor College of Medicine Human Genome Sequencing Center. The dynamin gene composition from sea lamprey was inferred from sequence alignment of draft 5.9-fold genome sequence (accessed via the UCSC browser - genome.ucsc.edu). When used as query, the respective mouse Dnm1, Dnm2 and Dnm3 peptide sequences corresponding to the assembly domain region each yielded significant alignments with only a single, approximately 20kb contig (Contig16000). This contig contained seven Dnm-like exons, with appropriate splice site recognition motifs, that was co-linear with mouse Dnm1 exons 8–13, including exons corresponding to Dnm1b (exon 10b) and Dnm1a (exon 10a) in the expected 5′-3′ arrangement. (C) Neighbor-joining best tree of dynamin peptides. Proportional number of differences is estimated at the bottom. Note the closer relationship between the two isoforms from sea lamprey and the respective Dnm1a and Dnm1b branches from more complex vertebrates. Also note the closer relationship between Dnm2 isoforms and invertebrate dynamin.

Cited by 0Open access

Conserved Sequence Motifs in Cellular RdRPs

Paula S Salgado (274264), Minni R. L Koivunen (274267), Eugene V Makeyev (274270) et al. · Figshare · 2015

Multiple sequence alignment of a representative subset of cRdRPs. Amino acid sequences of 30 cRdRPs from fungi from the groups of Ascomycota (Schizosaccharomyces pombe, Spo; Neurospora crassa, Ncr; and Gibberella zeae, Gze) and Basidiomycota (Cryptococcus neoformans, Cne), slime molds (Dictyostelium discoideum, Ddi), dicot plants (Arabidopsis thaliana, Ath; Solanum tuberosum, Stu; and Nicotiana tabacum, Ntu), monocot plants (Oryza sativa, Osa), protozoa (Entamoeba histolytica, Ehi), and nematodes (Caenorhabditis elegans, Cel) were aligned using standard settings of ClustalW algorithm. Local alignment was improved by manual editing. N. crassa QDE-1 protein sequence is shown on the top. N. crassa contains two additional non-allelic cRdRP genes—SAD-1 (essential for meiotic silencing by unpaired DNA ) and RdRP-3—that likely function in distinct cellular pathways. Invariant residues are shaded in black; other residues with 80% or more conservation are shaded in grey. Conserved sequence motifs comprising invariant residues are outlined: motif 1, red; motif 2, orange; motif 3, dark yellow; motif 4, purple; motif 5, violet; motif 6, light pink; and motif 7, blue. QDE-1 secondary structure elements are shown on top, coloured according to domain definition (slab, blue; catalytic, deep purple; neck, pink; and head, red). The identified double-psi β-barrels DPBB1 and DPBB2 are outlined by deep purple boxes. The flap sub-domain and the potential “bridge helices” are also represented by boxes, coloured light purple and grey, respectively. (914 KB DOC)

Cited by 0Open access

Conserved sequence across the Lepidoptera order.

Liangli Yang (5324732), Junjun Dai (5324735), Qiuping Gao (5324738) et al. · Figshare · 2020

(A) Intergenic spacer region alignment between trnS2 (UCN) and ND1 of several Lepidopterans. The framework ‘ATACTAA’ motif is conserved across the Lepidoptera order. (B) Intergenic overlap region alignment between ATP8 and ATP6 of several Lepidopterans. The bold ‘ATGATAA’ motif is the overlap region and it’s conserved across the Lepidoptera order. (C) Features present in the A+T-rich region of Orthaga olivacea Warre. The sequence is shown in the reverse strand. The ATAGA motif is bolded. The poly-T stretch is underlined. The single microsatellite T/A repeat sequence are double underlined.

Cited by 0Open access

DG-CST (Disease Gene Conserved Sequence Tags),

Angelo Boccia, Mauro Petrillo, Diego Di Bernardo et al. · 2004

Cited by 0

Conserved sequence motifs in the OR family

Zozulya, Sergey, Echeverri, Fernando, Nguyen, Trieu · Figshare · 2011

Copyright information:Taken from "The human olfactory receptor repertoire"Genome Biology 2001;2(6):research0018.1-research0018.12.Published online 1 Jun 2001PMCID:PMC33394.Copyright © 2001 Zozulya et al., licensee BioMed Central Ltd Sequence motifs based on analysis of the multiple sequence alignment of the full-length hOR repertoire are represented as 'sequence logo' [, ]. The height of each amino-acid symbol in a given position is proportional to its frequency of occurrence. The height of the sequence information part is computed as the relative entropy between the observed fractions of a given amino-acid symbol and the respective probabilities (assumed to be 0.05 for each amino acid). Locations of predicted transmembrane segments (TM1-7) as well as intracellular loops (IC1-3) and extracellular loops (EC1-3) are shown. TM boundaries are based on the predictions done using the neural network algorithm implemented with the PHDhtm and PHD topology programs [, , ]. The alignment was edited to adjust for OR length heterogeneity before sequence logo generation as described in Materials and methods. This figure is available as an additional data file in PDF format.

Cited by 0Open access

Conserved Sequence Motifs...................................................................................................................................509 The GTPase Cycle...............................................................................

Natalie Verstraeten, Maarten Fauvart, Jan Michiels · 2016

Cited by 0

Sequence Motif That Is Conserved in Evolution

K Strub, J Moss, P Walter et al. · 1991

evolution. contain a sequence motif that is conserved in exclusively in the Alu domain of SRP RNA and recognition particle (SRP) are contained heterodimeric protein subunit of the signal Binding sites of the 9- and 14-kilodalton

Cited by 0

Conserved Sequence Processing in Primate Frontal Cortex

Benjamin Wilson, William D. Marslen‐Wilson, Christopher I. Petkov · Trends in Neurosciences · 2017

Cited by 99Open access