Alignment statistic for identifying related protein sequences View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

1977-06

AUTHORS

G. William Moore, Morris Goodman

ABSTRACT

Closely related proteins show an obvious kinship by having numerous matching amino acids in their aligned sequences. Kinship between anciently separated proteins requires a statistical evaluation to rule out fortuitous similarities. A simple statistic is developed which assumes equal probability for all codon pairs, and a table of critical values for amino acid sequence alignments of lengthnments of length 200 or less is presented. Applying this statistic to V and C regions of immunoglobulin chains, aligned on the basis of shared features of three-dimensional structure, provides evidence that the V and C sequences descended from a common ancestor. Similarly the distant evolutionary relationship of dehydrogenases, flavdoxin, and subtilisin, suggested by structural alignments, is verified. On the other hand, the statistic does not verify a common evolutionary origin for the heme binding pocket in globins and cytochrome bs. Empirical evidence from the distribution of MMD values of amino acid pairs in comparisons of misaligned polypeptide chains and from Monte Carlo trials of sequences aligned with arbitrary gaps supports the validity of the statistic. More... »

PAGES

121-130

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/bf01732744

DOI

http://dx.doi.org/10.1007/bf01732744

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1016021604

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/864719


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0601", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biochemistry and Cell Biology", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Amino Acid Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Biological Evolution", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Flavodoxin", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Globins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Immunoglobulins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "L-Lactate Dehydrogenase", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Protein Conformation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Subtilisins", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Johns Hopkins Hospital", 
          "id": "https://www.grid.ac/institutes/grid.411935.b", 
          "name": [
            "Department of Pathology, The Johns Hopkins Hospital, 21205, Baltimore, Md., USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Moore", 
        "givenName": "G. William", 
        "id": "sg:person.01032646746.00", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01032646746.00"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Wayne State University", 
          "id": "https://www.grid.ac/institutes/grid.254444.7", 
          "name": [
            "Department of Anatomy, Wayne State University, School of Medicine, 540 E. Canfield Ave., 48201, Detroit, Michigan, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Goodman", 
        "givenName": "Morris", 
        "id": "sg:person.01023304676.50", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01023304676.50"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1073/pnas.69.1.4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007918384"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/250194a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013040231", 
          "https://doi.org/10.1038/250194a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.71.9.3440", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014786242"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0022-2836(70)90089-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017090906"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0022-2836(70)90057-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021169618"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0022-2836(72)90508-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026187273"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0022-2836(70)90372-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033069770"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0022-2836(66)80258-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033903030"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0022-2836(71)90390-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045478564"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.155.3760.279", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062490443"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1074932752", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "1977-06", 
    "datePublishedReg": "1977-06-01", 
    "description": "Closely related proteins show an obvious kinship by having numerous matching amino acids in their aligned sequences. Kinship between anciently separated proteins requires a statistical evaluation to rule out fortuitous similarities. A simple statistic is developed which assumes equal probability for all codon pairs, and a table of critical values for amino acid sequence alignments of lengthnments of length 200 or less is presented. Applying this statistic to V and C regions of immunoglobulin chains, aligned on the basis of shared features of three-dimensional structure, provides evidence that the V and C sequences descended from a common ancestor. Similarly the distant evolutionary relationship of dehydrogenases, flavdoxin, and subtilisin, suggested by structural alignments, is verified. On the other hand, the statistic does not verify a common evolutionary origin for the heme binding pocket in globins and cytochrome bs. Empirical evidence from the distribution of MMD values of amino acid pairs in comparisons of misaligned polypeptide chains and from Monte Carlo trials of sequences aligned with arbitrary gaps supports the validity of the statistic.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1007/bf01732744", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1016442", 
        "issn": [
          "0022-2844", 
          "1432-1432"
        ], 
        "name": "Journal of Molecular Evolution", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "2", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "9"
      }
    ], 
    "name": "Alignment statistic for identifying related protein sequences", 
    "pagination": "121-130", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "4c570499a641e4a682418494d40d923c11ae374c3b6c04fc7a28f48508ffa01d"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "864719"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "0360051"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/bf01732744"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1016021604"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/bf01732744", 
      "https://app.dimensions.ai/details/publication/pub.1016021604"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T09:38", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000346_0000000346/records_99833_00000001.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1007/BF01732744"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/bf01732744'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/bf01732744'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/bf01732744'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/bf01732744'


 

This table displays all metadata directly associated to this object as RDF triples.

144 TRIPLES      21 PREDICATES      48 URIs      29 LITERALS      17 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/bf01732744 schema:about N101e0808db5e464eab0fce593303cebf
2 N23b9c04df3414c679582d79d23d31bc5
3 N433d4e75373e46cc8236de12aa4c5bd4
4 N5025695527234858b0985018958bd0a0
5 Na5154194366c43b6bdf2e5977554e072
6 Na5b5e81c6fe94a4f8f14254edbe0debb
7 Na7a19de892e049d48cf9947492a134f7
8 Ndd52f149b6c04c7eb46bdfcfe55269d3
9 anzsrc-for:06
10 anzsrc-for:0601
11 schema:author Nd48ddf65024540d28431f33d6d6d9996
12 schema:citation sg:pub.10.1038/250194a0
13 https://app.dimensions.ai/details/publication/pub.1074932752
14 https://doi.org/10.1016/0022-2836(70)90057-4
15 https://doi.org/10.1016/0022-2836(70)90089-6
16 https://doi.org/10.1016/0022-2836(70)90372-4
17 https://doi.org/10.1016/0022-2836(71)90390-1
18 https://doi.org/10.1016/0022-2836(72)90508-6
19 https://doi.org/10.1016/s0022-2836(66)80258-9
20 https://doi.org/10.1073/pnas.69.1.4
21 https://doi.org/10.1073/pnas.71.9.3440
22 https://doi.org/10.1126/science.155.3760.279
23 schema:datePublished 1977-06
24 schema:datePublishedReg 1977-06-01
25 schema:description Closely related proteins show an obvious kinship by having numerous matching amino acids in their aligned sequences. Kinship between anciently separated proteins requires a statistical evaluation to rule out fortuitous similarities. A simple statistic is developed which assumes equal probability for all codon pairs, and a table of critical values for amino acid sequence alignments of lengthnments of length 200 or less is presented. Applying this statistic to V and C regions of immunoglobulin chains, aligned on the basis of shared features of three-dimensional structure, provides evidence that the V and C sequences descended from a common ancestor. Similarly the distant evolutionary relationship of dehydrogenases, flavdoxin, and subtilisin, suggested by structural alignments, is verified. On the other hand, the statistic does not verify a common evolutionary origin for the heme binding pocket in globins and cytochrome bs. Empirical evidence from the distribution of MMD values of amino acid pairs in comparisons of misaligned polypeptide chains and from Monte Carlo trials of sequences aligned with arbitrary gaps supports the validity of the statistic.
26 schema:genre research_article
27 schema:inLanguage en
28 schema:isAccessibleForFree false
29 schema:isPartOf Nccccbe11831e4785a46cc94597f73617
30 Ne4787e7ff98a4e779ee845da666797fa
31 sg:journal.1016442
32 schema:name Alignment statistic for identifying related protein sequences
33 schema:pagination 121-130
34 schema:productId N47efec6aedc643778c5f4b0cb0302f50
35 N6ab8d7c95fd94bd6bfaeb08185cd1785
36 N711594c109b74ef689e7d09398bd0e05
37 N8cb46814d23b488e9a148b6365a58c82
38 Nbcdd36b1f0c446f292a0ea438641f664
39 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016021604
40 https://doi.org/10.1007/bf01732744
41 schema:sdDatePublished 2019-04-11T09:38
42 schema:sdLicense https://scigraph.springernature.com/explorer/license/
43 schema:sdPublisher N6540a316ae4b4a8881599c5d9b88d736
44 schema:url http://link.springer.com/10.1007/BF01732744
45 sgo:license sg:explorer/license/
46 sgo:sdDataset articles
47 rdf:type schema:ScholarlyArticle
48 N101e0808db5e464eab0fce593303cebf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
49 schema:name Flavodoxin
50 rdf:type schema:DefinedTerm
51 N23b9c04df3414c679582d79d23d31bc5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
52 schema:name Immunoglobulins
53 rdf:type schema:DefinedTerm
54 N433d4e75373e46cc8236de12aa4c5bd4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
55 schema:name Protein Conformation
56 rdf:type schema:DefinedTerm
57 N47efec6aedc643778c5f4b0cb0302f50 schema:name doi
58 schema:value 10.1007/bf01732744
59 rdf:type schema:PropertyValue
60 N5025695527234858b0985018958bd0a0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
61 schema:name Subtilisins
62 rdf:type schema:DefinedTerm
63 N6540a316ae4b4a8881599c5d9b88d736 schema:name Springer Nature - SN SciGraph project
64 rdf:type schema:Organization
65 N6ab8d7c95fd94bd6bfaeb08185cd1785 schema:name nlm_unique_id
66 schema:value 0360051
67 rdf:type schema:PropertyValue
68 N711594c109b74ef689e7d09398bd0e05 schema:name readcube_id
69 schema:value 4c570499a641e4a682418494d40d923c11ae374c3b6c04fc7a28f48508ffa01d
70 rdf:type schema:PropertyValue
71 N8cb46814d23b488e9a148b6365a58c82 schema:name pubmed_id
72 schema:value 864719
73 rdf:type schema:PropertyValue
74 Na5154194366c43b6bdf2e5977554e072 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
75 schema:name Biological Evolution
76 rdf:type schema:DefinedTerm
77 Na5b5e81c6fe94a4f8f14254edbe0debb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
78 schema:name Amino Acid Sequence
79 rdf:type schema:DefinedTerm
80 Na7a19de892e049d48cf9947492a134f7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
81 schema:name Globins
82 rdf:type schema:DefinedTerm
83 Nb2c9444731bd4f389f4febd45d0c2104 rdf:first sg:person.01023304676.50
84 rdf:rest rdf:nil
85 Nbcdd36b1f0c446f292a0ea438641f664 schema:name dimensions_id
86 schema:value pub.1016021604
87 rdf:type schema:PropertyValue
88 Nccccbe11831e4785a46cc94597f73617 schema:volumeNumber 9
89 rdf:type schema:PublicationVolume
90 Nd48ddf65024540d28431f33d6d6d9996 rdf:first sg:person.01032646746.00
91 rdf:rest Nb2c9444731bd4f389f4febd45d0c2104
92 Ndd52f149b6c04c7eb46bdfcfe55269d3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
93 schema:name L-Lactate Dehydrogenase
94 rdf:type schema:DefinedTerm
95 Ne4787e7ff98a4e779ee845da666797fa schema:issueNumber 2
96 rdf:type schema:PublicationIssue
97 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
98 schema:name Biological Sciences
99 rdf:type schema:DefinedTerm
100 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
101 schema:name Biochemistry and Cell Biology
102 rdf:type schema:DefinedTerm
103 sg:journal.1016442 schema:issn 0022-2844
104 1432-1432
105 schema:name Journal of Molecular Evolution
106 rdf:type schema:Periodical
107 sg:person.01023304676.50 schema:affiliation https://www.grid.ac/institutes/grid.254444.7
108 schema:familyName Goodman
109 schema:givenName Morris
110 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01023304676.50
111 rdf:type schema:Person
112 sg:person.01032646746.00 schema:affiliation https://www.grid.ac/institutes/grid.411935.b
113 schema:familyName Moore
114 schema:givenName G. William
115 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01032646746.00
116 rdf:type schema:Person
117 sg:pub.10.1038/250194a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013040231
118 https://doi.org/10.1038/250194a0
119 rdf:type schema:CreativeWork
120 https://app.dimensions.ai/details/publication/pub.1074932752 schema:CreativeWork
121 https://doi.org/10.1016/0022-2836(70)90057-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021169618
122 rdf:type schema:CreativeWork
123 https://doi.org/10.1016/0022-2836(70)90089-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017090906
124 rdf:type schema:CreativeWork
125 https://doi.org/10.1016/0022-2836(70)90372-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033069770
126 rdf:type schema:CreativeWork
127 https://doi.org/10.1016/0022-2836(71)90390-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045478564
128 rdf:type schema:CreativeWork
129 https://doi.org/10.1016/0022-2836(72)90508-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026187273
130 rdf:type schema:CreativeWork
131 https://doi.org/10.1016/s0022-2836(66)80258-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033903030
132 rdf:type schema:CreativeWork
133 https://doi.org/10.1073/pnas.69.1.4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007918384
134 rdf:type schema:CreativeWork
135 https://doi.org/10.1073/pnas.71.9.3440 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014786242
136 rdf:type schema:CreativeWork
137 https://doi.org/10.1126/science.155.3760.279 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062490443
138 rdf:type schema:CreativeWork
139 https://www.grid.ac/institutes/grid.254444.7 schema:alternateName Wayne State University
140 schema:name Department of Anatomy, Wayne State University, School of Medicine, 540 E. Canfield Ave., 48201, Detroit, Michigan, USA
141 rdf:type schema:Organization
142 https://www.grid.ac/institutes/grid.411935.b schema:alternateName Johns Hopkins Hospital
143 schema:name Department of Pathology, The Johns Hopkins Hospital, 21205, Baltimore, Md., USA
144 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...