---
_id: '2250'
abstract:
- lang: eng
  text: The genome sequences of new viruses often contain many "orphan"
    or "taxon-specific" proteins apparently lacking homologs. However, because
    viral proteins evolve very fast, commonly used sequence similarity detection methods
    such as BLAST may overlook homologs. We analyzed a data set of proteins from RNA
    viruses characterized as "genus specific" by BLAST. More powerful methods
    developed recently, such as HHblits or HHpred (available through web-based, user-friendly
    interfaces), could detect distant homologs of a quarter of these proteins, suggesting
    that these methods should be used to annotate viral genomes. In-depth manual analyses
    of a subset of the remaining sequences, guided by contextual information such
    as taxonomy, gene order, or domain cooccurrence, identified distant homologs of
    another third. Thus, a combination of powerful automated methods and manual analyses
    can uncover distant homologs of many proteins thought to be orphans. We expect
    these methodological results to be also applicable to cellular organisms, since
    they generally evolve much more slowly than RNA viruses. As an application, we
    reanalyzed the genome of a bee pathogen, Chronic bee paralysis virus (CBPV). We
    could identify homologs of most of its proteins thought to be orphans; in each
    case, identifying homologs provided functional clues. We discovered that CBPV
    encodes a domain homologous to the Alphavirus methyltransferase-guanylyltransferase;
    a putative membrane protein, SP24, with homologs in unrelated insect viruses and
    insect-transmitted plant viruses having different morphologies (cileviruses, higreviruses,
    blunerviruses, negeviruses); and a putative virion glycoprotein, ORF2, also found
    in negeviruses. SP24 and ORF2 are probably major structural components of the
    virionsd.
author:
- first_name: Durga
  full_name: Kuchibhatla, Durga
  last_name: Kuchibhatla
- first_name: Westley
  full_name: Sherman, Westley
  last_name: Sherman
- first_name: Betty
  full_name: Chung, Betty
  last_name: Chung
- first_name: Shelley
  full_name: Cook, Shelley
  last_name: Cook
- first_name: Georg
  full_name: Schneider, Georg
  id: 329095A0-F248-11E8-B48F-1D18A9856A87
  last_name: Schneider
- first_name: Birgit
  full_name: Eisenhaber, Birgit
  last_name: Eisenhaber
- first_name: David
  full_name: Karlin, David
  last_name: Karlin
citation:
  ama: Kuchibhatla D, Sherman W, Chung B, et al. Powerful sequence similarity search
    methods and in-depth manual analyses can identify remote homologs in many apparently
    “orphan” viral proteins. <i>Journal of Virology</i>. 2014;88(1):10-20. doi:<a
    href="https://doi.org/10.1128/JVI.02595-13">10.1128/JVI.02595-13</a>
  apa: Kuchibhatla, D., Sherman, W., Chung, B., Cook, S., Schneider, G., Eisenhaber,
    B., &#38; Karlin, D. (2014). Powerful sequence similarity search methods and in-depth
    manual analyses can identify remote homologs in many apparently “orphan” viral
    proteins. <i>Journal of Virology</i>. ASM. <a href="https://doi.org/10.1128/JVI.02595-13">https://doi.org/10.1128/JVI.02595-13</a>
  chicago: Kuchibhatla, Durga, Westley Sherman, Betty Chung, Shelley Cook, Georg Schneider,
    Birgit Eisenhaber, and David Karlin. “Powerful Sequence Similarity Search Methods
    and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently ‘Orphan’
    Viral Proteins.” <i>Journal of Virology</i>. ASM, 2014. <a href="https://doi.org/10.1128/JVI.02595-13">https://doi.org/10.1128/JVI.02595-13</a>.
  ieee: D. Kuchibhatla <i>et al.</i>, “Powerful sequence similarity search methods
    and in-depth manual analyses can identify remote homologs in many apparently ‘orphan’
    viral proteins,” <i>Journal of Virology</i>, vol. 88, no. 1. ASM, pp. 10–20, 2014.
  ista: Kuchibhatla D, Sherman W, Chung B, Cook S, Schneider G, Eisenhaber B, Karlin
    D. 2014. Powerful sequence similarity search methods and in-depth manual analyses
    can identify remote homologs in many apparently ‘orphan’ viral proteins. Journal
    of Virology. 88(1), 10–20.
  mla: Kuchibhatla, Durga, et al. “Powerful Sequence Similarity Search Methods and
    In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently ‘Orphan’
    Viral Proteins.” <i>Journal of Virology</i>, vol. 88, no. 1, ASM, 2014, pp. 10–20,
    doi:<a href="https://doi.org/10.1128/JVI.02595-13">10.1128/JVI.02595-13</a>.
  short: D. Kuchibhatla, W. Sherman, B. Chung, S. Cook, G. Schneider, B. Eisenhaber,
    D. Karlin, Journal of Virology 88 (2014) 10–20.
date_created: 2018-12-11T11:56:34Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:17Z
day: '01'
ddc:
- '570'
department:
- _id: MD
doi: 10.1128/JVI.02595-13
file:
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file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: '        88'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 10 - 20
publication: Journal of Virology
publication_identifier:
  issn:
  - 0022538X
publication_status: published
publisher: ASM
publist_id: '4698'
pubrep_id: '417'
quality_controlled: '1'
scopus_import: 1
status: public
title: Powerful sequence similarity search methods and in-depth manual analyses can
  identify remote homologs in many apparently "orphan" viral proteins
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 88
year: '2014'
...