Table 3.

Locations of HHV-6B ORFs and relative similarities of HHV-6B genes with their HHV-6A and HHV-7 homologs

ORFaSStartbEndc% DNA identity with HHV-6A homologdCodons%S/%/I with HHV-6A homologeSubstitutionsf%S/%I with HHV-7 homologgImplied functionh
KaKs
DR1EX158384188.48690.7/87.20.0920.14650.9/47.6HCMV US22 gene family
DR1EX2955297290.067284.0/82.450.7/45.4
DR3Ci 3325272690.820087.0/86.40.0720.174
B130223498159
B23536377279
DR6EX15027533089.110186.1/84.10.1120.22355.4/53.5HCMV US22 gene family, transactivator
DR6EX26329720088.829084.3/82.269.1/62.6
B37349752559
B4C94928914193Membrane protein?
B59522975879
U2C10715962792.436392.1/91.50.0480.19954.7/47.8HCMV US22 gene family
U3C122051104892.438689.8/89.30.0640.21156.1/46.8HCMV US22 gene family, transactivator
U4C140401243696.953598.9/98.70.0060.10168.8/58.9
U7EX1C169591589094.935698.4/97.50.0200.14174.7/61.6HCMV US22 gene family
U7EX2C158001416294.754695.2/94.50.0260.15061.0/51.1
U6156031580695.16897.1/97.10.0170.113
U8C181981696695.041196.4/95.50.0230.13062.1/50.8HCMV US22 gene family
U9C184931818295.510494.2/94.20.0260.083
U10185432005192.950396.6/94.00.0330.19461.9/49.4
U11C225341996189.285885.6/81.20.1100.13440.9/29.8Antigenic virion protein 101K
U12EX1226362266897.011100/1000.0400.13572.7/54.5G-protein-coupled receptor
U12EX2227462332793.419493.8/92.260.6/46.6
U13238562417696.210793.4/92.50.0370.06144.9/35.7
U14242772610690.561089.3/85.70.0820.15056.7/49.9
U15EX1C270482673194.010691.4/86.70.0470.08876.4/67.9HCMV UL25/UL35 gene family
U15EX2C267522650094.524100/95.883.3/75.0
U15EX3C263282614695.16196.7/91.782.0/75.4
U17EX1C284212819395.27694.7/94.70.0260.13354.9/43.7HCMV US22 gene family, IE-B
U17EX2C281052733394.625796.1/94.966.7/56.5
U18C304852960493.729490.8/88.70.0550.07057.5/47.0IE-B
U19C319203075494.238992.0/91.50.0430.09841.5/35.1IE-B
U20C334493214894.243495.6/95.60.0450.12131.8/22.2
U21C349543345593.250091.0/89.80.0500.12142.8/31.6
U22C354593485495.420291.2/89.60.0280.097
U23C363863549092.629994.6/94.10.0630.11626.9/20.9
U24C367773651492.78888.3/82.70.0800.05446.2/31.2
U24AC369693679993.55794.7/91.20.0420.13340.3/28.1
U25C379363698997.431699.4/98.10.0090.07545.0/31.2HCMV US22 gene family
U26C389313804795.129593.8/92.90.0330.09260.5/47.4
U27C400193892295.536697.3/95.60.0210.11245.7/31.1Polymerase processivity factor
U28C425494013895.880497.1/95.90.0190.10657.7/46.6Large ribonucleotide reductase
U29C434714257596.029997.6/96.10.0200.10366.3/51.9Capsid assembly and DNA maturation
U30429994624494.8108295.2/93.20.0330.10658.4/46.3
U31462655249594.8207795.3/93.40.0320.10757.4/46.5Large tegument protein
U32C528415257595.88996.6/96.60.0170.12071.9/65.2
U33C542555284697.147098.3/98.10.0090.08270.6/59.4
U34C550365420995.227695.3/94.20.0280.09765.1/57.0
U35C553735505697.810698.1/98.10.0090.04668.9/59.2
U36553725682396.748497.9/97.50.0120.08768.9/58.1
U37568305762197.026498.1/97.00.0140.07471.8/61.8
U38C607085767396.2101298.7/97.90.0100.11875.9/67.0DNA polymerase
U39C632006071196.483097.0/96.10.0190.10965.8/56.7Glycoprotein B
U40C653346315796.972699.2/98.80.0080.09367.8/55.9Transport/capsid assembly
U41C687406534597.3113299.3/98.80.0060.07078.7/68.5Major DNA binding protein
U42C716537010695.551696.1/95.50.0240.10566.6/56.0Transactivator
U43C744607188197.386098.8/97.70.0100.06870.9/61.0Helicase/primase complex
U44745017519395.923198.1/96.70.0140.12170.4/58.6
U45C762737514695.837695.5/94.40.0320.07459.2/50.5
U46763467659795.28494.1/94.10.0330.08661.9/51.2
U47C789997678693.473889.5/87.20.0650.08031.8/23.9Glycoprotein 0
U48C813497926895.369495.8/94.20.0280.10352.2/39.0Glycoprotein H
U49815088226396.925297.6/97.20.0150.05960.7/52.7
U50820438370796.355598.9/97.30.0150.09065.4/54.7Virion protein
U51838088471094.930195.7/94.00.0310.09648.6/36.1G-protein-coupled receptor
U52C855088473596.625898.1/97.30.0120.08168.1/56.3
U53855158709896.252897.4/96.80.0170.09859.6/51.1Proteinase
U54C887158733988.645984.5/79.70.1200.11855.3/44.5Virion transactivator
U55C902718879695.149294.9/93.60.0320.108(A)44.2/32.4
(B)33.9/21.2
U56C911629027598.129699.0/98.00.0100.05274.7/65/2Capsid protein
U57C952019116796.6134598.1/97.80.0110.08777.9/68.6Major capsid protein
U58952139752895.877297.5/96.90.0150.10969.8/61.4
U59975289857795.735096.0/95.10.0220.10050.9/39.9
U62997169997698.08796.5/96.50.0190.06265.8/52.1
U639992110057497.521899.1/99.10.0040.09073.9/67.3
U6410055510188095.544294.1/93.70.0310.09352.6/40.0
U6510184010284492.833589.0/85.70.0730.07469.1/60.0
U66EX1C10378410291297.529199.0/99.00.0020.08072.1/63.8Putative terminase
U66EX2C997049858097.9375100/10086.3/78.3
U6710375610481496.735397.5/96.60.0160.07363.7/53.2
U6810481710515895.911496.5/94.70.0260.12062.3/49.1
U6910516410685294.856396.4/94.70.0270.11463.6/53.7Phosphotransferase; ganciclovir kinase
U7010686310832695.948897.1/96.10.0200.10064.6/51.8Alkaline exonuclease
U7110826610850892.68190.9/89.60.0600.13656.2/52.1Myristylated virion protein
U72C10962710859696.634498.3/97.10.0130.08272.4/58.7Glycoprotein M
U7310964011197997.378098.6/97.60.0140.06767.3/57.9Origin binding protein
U7411195111393696.166297.6/96.20.0190.08854.6/41.3Helicase/primase complex
U75C11472311397796.124997.2/96.00.0210.10355.8/45.8
U76C11662011463597.166198.9/98.60.0070.09670.4/58.9
U7711641511888697.382499.3/98.90.0050.08382.7/75.5Helicase/primase complex
B611913911937579
B712083612106075
U79EX112148612211687.521084.8/76.70.0940.10369.3/52.7Role in DNA replication
U79EX212221312241292.46689.2/84.657.1/47.6
U79EX312249512310393.820388.9/86.945.4/37.9
U81C12391712315395.225595.7/94.50.0300.10969.2/58.9Uracil-DNA glycosylase
U82C12474512399695.525095.2/94.00.0290.07749.6/37.4Glycoprotein L
U8312482112515992.411387.6/85.60.0710.098Intercrine cytokine
U84C12629612527194.234292.4/90.60.0480.08151.7/42.4
U85C12720212632794.729193.1/91.70.0440.08346.9/36.8OX-2 homology, glycoprotein
U86C13190112734285.9152079.2/74.50.1510.19835.3/29.5IE-A
U90EX1C13843613834281.37573.7/68.40.1710.12742.8/35.7IE-A (IE1), transactivator
U90EX2C13825413804380.97070.3/67.267.1/57.1
U90EX3C13793213500685.897576.7/71.532.9/25.2
U91EX113859113881676.37567.8/57.10.3010.24633.3/25.0IE-A
U91EX213892613916782.08069.2/67.945.6/40.0
B8C142766141972265
U94C14456514309696.549098.4/97.60.0110.089Parvovirusrep homolog
U9514464014827584.0121272.9/69.00.1880.15033.4/26.7HCMV US22 gene family
U100EX1C15232515194083.412878.1/73.40.1150.17827.2/19.7Spliced envelope glycoprotein
U100EX2C15180715152687.69384.9/81.753.8/38.7
U100EX3C15112115078688.711182.9/79.340.9/32.7
U100EX4C15066415058788.52596.0/88.044.0/40.0
U100EX5C15047615036992.63588.6/80.034.3/28.6
U100EX6C15027215015995.63791.9/91.948.6/37.8
U100EX7C15000814984889.45388.7/83.035.3/27.4
U100EX8C149341149332100.03100/100
U100EX9C14916914904194.64292.8/90.535.7/23.8
U100EX10C14891114866886.58183.9/76.524.0/13.3
B9C153252152935106
DR1EX115390415416288.48690.7/87.20.0920.14650.0/47.6HCMV US22 gene family
DR1EX215427615629390.067284.0/82.450.7/45.4
DR3C15664615604790.820087.0/86.4
B1156343156819159
B215685715709379
DR6EX115834815865189.110186.1/84.10.1120.22355.4/53.5HCMV US22 gene family
DR6EX215965016052188.829084.3/82.269.1/62.6
B316067016084659
  • a HHV-6B ORFs are named after their HHV-6A counterparts (19), except for spliced genes where the ORF is given the name of the 5′-proximal ORF. Based on the interpretation of the HHV-7 sequence by Megaw et al. (37), some of the ORFs described by Gompels et al. (19) are predicted to be exons: DR2 as DR1EX2; DR7 as DR6EX2; U5 as U7EX2; U16 as U17EX2; U60 as U66EX2; U80 as U79EX3; U89 as U90EX3; and U96, U97, U98, and U99 as U100EX10, EX7, EX3, and EX2, respectively. ORFs B1 to B9 are unique to HHV-6B.

  • b First N-terminal methionine or in spliced genes first nucleotide of predicted exon.

  • c Last nucleotide of the last codon of ORF or exon.

  • d Determined by using GAP with gap and length weights of 50 and 3, respectively.

  • e Percent amino acid similarity (%S) and percent amino acid identity (%I) were determined by using GAP with gap and length weights of 12 and 4, respectively.

  • f Nonsynonymous (Ka) and synonymous (Ks) substitutions between HHV-6B and HHV-6A coding regions were estimated by using DIVERGE. Ka and Ks values given for spliced genes were determined by using the spliced coding sequence and listed in the first exon.

  • g HHV-7 ORFs used in the alignments are from HHV-7(JI) as described by Nicholas (41) plus additional exons described by Megaw et al. (37). Prefixes (A) and (B) denote HHV-7 ORFs U55A and U55B, respectively.

  • h Functions of analogous genes were inferred from previous analyses (8, 19, 22, 37, 41).

  • i ORFs encoded on the complementary strand are indicated by C.