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clustalw multiple alignment function  (MacVector inc)

 
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    Structured Review

    MacVector inc clustalw multiple alignment function
    Amino acid sequence alignments of RmAQP1-3 with putative aquaporins from other tick species. Alignment was by the <t>ClustalW</t> multiple alignment function of MacVector 12.7.5 using the Gonnet matrix with open gap penalty of 10 and extend gap penalty of 0.05. Determination of amino acid similarity was by chemical properties of amino acid side chains with DE, AGILV, NQ, FWY, RHK, ST, CM, and P comprising the groups considered as conservative substitutions. The accession numbers for the putative tick aquaporins from R. appendiculatus , R. sanguineus , I. scapularis , I. ricinus , and D. variabilis are CD780384, CAR66115, XP_002399794, CAX48964, and ABI53034, respectively. One member each from the human aquaporin families 3 (NP 004916) and 7 (NP 001161) are also included in the alignment. The RmAQP1 was used as the model for comparing other sequences, with identities indicated by colon (:) and similarities by period (.). In the summary line below the 10 aligned sequences, a colon (:) notes amino acid positions where all 10 sequences contain the identical amino acid, a period (.) indicates all 10 sequences contain identical or similar amino acids, and an asterisk (*) indicates 9 of the 10 aligned sequences have identical or similar amino acids. Gaps inserted to optimize alignments are indicated by a dash (−). The shaded portions of the RmAQP1 sequence indicate the six predicted transmembrane helical regions.
    Clustalw Multiple Alignment Function, supplied by MacVector inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/clustal+w+function/clustalw+multiple+alignment+function/pmc04200143-183-4-9
    Average 90 stars, based on 1 article reviews
    clustalw multiple alignment function - by Bioz Stars, 2026-09
    90/100 stars

    Images

    1) Product Images from "Rhipicephalus ( Boophilus ) microplus aquaporin as an effective vaccine antigen to protect against cattle tick infestations"

    Article Title: Rhipicephalus ( Boophilus ) microplus aquaporin as an effective vaccine antigen to protect against cattle tick infestations

    Journal: Parasites & Vectors

    doi: 10.1186/s13071-014-0475-9

    Amino acid sequence alignments of RmAQP1-3 with putative aquaporins from other tick species. Alignment was by the ClustalW multiple alignment function of MacVector 12.7.5 using the Gonnet matrix with open gap penalty of 10 and extend gap penalty of 0.05. Determination of amino acid similarity was by chemical properties of amino acid side chains with DE, AGILV, NQ, FWY, RHK, ST, CM, and P comprising the groups considered as conservative substitutions. The accession numbers for the putative tick aquaporins from R. appendiculatus , R. sanguineus , I. scapularis , I. ricinus , and D. variabilis are CD780384, CAR66115, XP_002399794, CAX48964, and ABI53034, respectively. One member each from the human aquaporin families 3 (NP 004916) and 7 (NP 001161) are also included in the alignment. The RmAQP1 was used as the model for comparing other sequences, with identities indicated by colon (:) and similarities by period (.). In the summary line below the 10 aligned sequences, a colon (:) notes amino acid positions where all 10 sequences contain the identical amino acid, a period (.) indicates all 10 sequences contain identical or similar amino acids, and an asterisk (*) indicates 9 of the 10 aligned sequences have identical or similar amino acids. Gaps inserted to optimize alignments are indicated by a dash (−). The shaded portions of the RmAQP1 sequence indicate the six predicted transmembrane helical regions.
    Figure Legend Snippet: Amino acid sequence alignments of RmAQP1-3 with putative aquaporins from other tick species. Alignment was by the ClustalW multiple alignment function of MacVector 12.7.5 using the Gonnet matrix with open gap penalty of 10 and extend gap penalty of 0.05. Determination of amino acid similarity was by chemical properties of amino acid side chains with DE, AGILV, NQ, FWY, RHK, ST, CM, and P comprising the groups considered as conservative substitutions. The accession numbers for the putative tick aquaporins from R. appendiculatus , R. sanguineus , I. scapularis , I. ricinus , and D. variabilis are CD780384, CAR66115, XP_002399794, CAX48964, and ABI53034, respectively. One member each from the human aquaporin families 3 (NP 004916) and 7 (NP 001161) are also included in the alignment. The RmAQP1 was used as the model for comparing other sequences, with identities indicated by colon (:) and similarities by period (.). In the summary line below the 10 aligned sequences, a colon (:) notes amino acid positions where all 10 sequences contain the identical amino acid, a period (.) indicates all 10 sequences contain identical or similar amino acids, and an asterisk (*) indicates 9 of the 10 aligned sequences have identical or similar amino acids. Gaps inserted to optimize alignments are indicated by a dash (−). The shaded portions of the RmAQP1 sequence indicate the six predicted transmembrane helical regions.

    Techniques Used: Sequencing

    Related Articles

    Sequencing:

    Article Title: Rhipicephalus ( Boophilus ) microplus aquaporin as an effective vaccine antigen to protect against cattle tick infestations
    Article Snippet: Alignment was by the ClustalW multiple alignment function of MacVector 12.7.5 using the Gonnet matrix with open gap penalty of 10 and extend gap penalty of 0.05.



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    The feature of selected VNARs ( a ) The characterization of selected clone from each pool. n.d. = not detected. ( b ) VNAR amino acid sequence of selected clone. Complementarity determining region 1 (CDR1), Hyper variable region 2 (HV2), HV4 and CDR3 are expressed under the sequences. The sequences were expressed by using BioEdit version 7.2.5. Cysteine residues are highlighted in yellow. Positively charged amino acids, negatively charged amino acids, and hydrophobic amino acids in CDR3 are shown in red, green, and blue, respectively. ( c ) Sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) of the selected clones under non-reducing condition. M: Protein Marker.

    Journal: Marine Drugs

    Article Title: Novel Approach for Obtaining Variable Domain of New Antigen Receptor with Different Physicochemical Properties from Japanese Topeshark ( Hemitriakis japanica )

    doi: 10.3390/md21110550

    Figure Lengend Snippet: The feature of selected VNARs ( a ) The characterization of selected clone from each pool. n.d. = not detected. ( b ) VNAR amino acid sequence of selected clone. Complementarity determining region 1 (CDR1), Hyper variable region 2 (HV2), HV4 and CDR3 are expressed under the sequences. The sequences were expressed by using BioEdit version 7.2.5. Cysteine residues are highlighted in yellow. Positively charged amino acids, negatively charged amino acids, and hydrophobic amino acids in CDR3 are shown in red, green, and blue, respectively. ( c ) Sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) of the selected clones under non-reducing condition. M: Protein Marker.

    Article Snippet: CDR3 sequence comparison figures were created using the alignment function (Clustal W [ ]) in BioEdit version 7.2.5 (Bioedit, Manchester, UK).

    Techniques: Sequencing, Polyacrylamide Gel Electrophoresis, SDS Page, Clone Assay, Marker