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Research Article

PH1: An Archaeovirus of Haloarcula hispanica Related to SH1 and HHIV-2

Table 4

ORF annotations of the halovirus PH1 genome.

ORFaPositionbLocus tagLengthc (aa)pKiSimilarity/characteristics

1441–605HhPH1_gp01504.376% aa similarity to SH1 ORF2 (YP_271859)
2602–802HhPH1_gp026610.980% aa similarity to SH1 ORF3 (YP_271860)
3802–1059HhPH1_gp03853.985% aa similarity to SH1 ORF4 (YP_271861). 44% similarity to HHIV-2 protein 1
41056–1283HhPH1_gp04753.985% aa identity to SH1 ORF5 (YP_271862). Predicted coiled-coil region.
51276–1686HhPH1_gp051364.980% aa similarity to SH1 ORF6 (YP_271863). Two transmembrane domains. Also related to HHIV-2 protein 2 (38%, AFD02283) and to Halobiforma lacisalsi ORF ZP_09950018 (35%)
61683–1829HhPH1_gp06486.181% aa similarity to SH1 ORF7 (YP_271864). Predicted signal sequence (SignalP).
71822–2130HhPH1_gp071025.891% aa similarity to SH1 ORF8 (YP_271865) and 86% to HHIV-2 putative protein 3 (AFD02284). Other homologs include Nocardia protein pnf2110 (YP_122060.1), Hrr. lacusprofundi Hlac_0751 (YP_002565421.1), ORFs in actinophage VWB (AAR29707), Frankia (EAN11657), and gp40 of Mycobacterium phage Dori (AER47690)
82123–2383HhPH1_gp08864.290% aa similarity to SH1 ORF9 (YP_271866)
92380–2714HhPH1_gp091115.288% aa similarity to SH1 ORF11 (YP_271868) and also similarity to putative protein 4 of HHIV-2 (AFD02285) HlacAJ_19877 of Hbf. lacisalsi AJ5 (ZP_09950016)
102861–3004HhPH1_gp104710.4Weak similarity to SH1 ORF12 (YP_271869) only over the N-terminal 18 residues
113029–3100HhPH1_gp112312.3Not present in SH1 or HHIV-2
123134–7453HhPH1_gp1214394.2Capsid protein VP1. 72% similarity to SH1 VP1 (ORF 13, YP_271870); HHIV-2 VP1 (AFD02286); HlacAJ_19872 Hbf. lacisalsi AJ5. Predicted helix-turn-helix and RuvA-like domain (InterproScan)
137505–8227HhPH1_gp132405.4Predicted P-loop ATPase domain (COG0433). 92% aa similarity to SH1 ORF17 (YP_271874) and also similarity to putative ATPase of HHIV-2 (AFD02288); ATPase of Haladapatus paucihalophilus DX253 (ZP_08046180); HlacAJ_19867 of Hbf. lacisalsi (ZP_09950014)
148419–8228cHhPH1_gp14635.143% aa similarity to SH1 ORF18 (YP_271875). Alanine-rich. Central transmembrane domain (Phobius)
158856–8416cHhPH1_gp151464.192% aa similarity to SH1 ORF19 (YP_271876) and also to HHIV-2 putative protein 9 (AFD02290); HlacAJ_19857 of Hbf. lacisalsi AJ5; ZOD2009_19093 of Hap. paucihalophilus
168853–9500cHhPH1_gp162153.965% aa similarity to SH1 ORF20 (YP_271877) and also to putative protein 11 of HHIV-2 (AFD02292); ZOD2009_19098 of Hap. paucihalophilus; HlacAJ_19852 Hbf. lacisalsi AJ5. C-terminal transmembrane domain (Phobius)
179500–9919cHhPH1_gp171394.179% aa similarity to SH1 ORF21 (YP_271878) and also to putative protein 12 of HHIV-2 (AFD02293); hypothetical protein HlacAJ_19847 of Hbf. lacisalsi (ZP_09950010). Transmembrane domain (Phobius)
189923–10594cHhPH1_gp182234.383% aa similarity to SH1 ORF22 (YP_271879) and also to putative protein 13 of HHIV-2 (AFD02294), ZOD2009_19108 of Hap. paucihalophilus; HlacAJ_19842 of Hbf. lacisalsi. Predicted signal sequence (signalP). Contains 4 CxxC motifs.
1910659–10943HhPH1_gp199410.4Capsid protein VP12 (ORF19). 91% aa similarity to SH1 VP12 (ORF23, YP_271880) and also to VP12 of HHIV-2 (AFD02295) and HlacAJ_19837 of Hbf. lacisalsi; ZOD2009_19113 of Hap. paucihalophilus. Two transmembrane domains (Phobius)
2010960–11517HhPH1_gp201854.4Capsid protein VP7 (ORF20). 98% aa similarity to SH1 VP7 (ORF24, YP_271881) and also to VP7 of HHIV-2 (AFD02296); ZOD2009_19118 of Hap. paucihalophilus; HlacAJ_19832 of Hbf. lacisalsi AJ5
2111519–12217HhPH1_gp212324.1Capsid protein VP4 (ORF21). 94% aa similarity to SH1 ORF25 (YP_271882) and also to VP4 of HHIV-2 (AFD02297); ZOD2009_19123 of Hap. paucihalophilus; HlacAJ_19827 of Hbf. lacisalsi AJ5
2212233–12454HhPH1_gp22733.981% aa similarity to SH1 ORF26 (YP_271883) and also to putative protein 17 of HHIV-2 (AFD02298);
2312458–12697HhPH1_gp23794.878% aa similarity to SH1 capsid protein VP13 (ORF27, YP_271884) and also to VP13 of HHIV-2 (AFD02299). Predicted coil-coil domain. Predicted C-terminal transmembrane domain (Phobius).
2412701–15064HhPH1_gp247873.9Capsid protein VP2 (ORF24). 75% aa similarity to SH1 VP2 (ORF28, YP_271885) and to VP2 of HHIV-2 (AFD02300); ZOD2009_19133 of Hap. paucihalophilus (ZP_08046189).
2515065–15961HhPH1_gp252984.5Putative capsid protein VP5 (ORF25). 81% aa similarity to SH1 VP5 (ORF29, YP_271886) and to HHIV-2 VP5 (AFD02301); HlacAJ_19807 of Hbf lacisalsi AJ5; ZOD2009_19133 of Hap. paucihalophilus.
2615964–16446HhPH1_gp261604.673% aa similarity to SH1 capsid protein VP10 (ORF30, YP_271887) and to VP10 of HHIV-2 (AFD02302); ZOD2009_19138 of Hap. paucihalophilus; HlacAJ_19802 of Hbf. lacisalsi. Predicted C-terminal transmembrane domain (TMHMM).
2716446–16895HhPH1_gp271494.2Capsid protein VP9 (ORF27). 94% aa similarity to SH1 VP9 (ORF31, YP_271888) and to ZOD2009_19143 of Hap. paucihalophilus (ZP_08046191)
2816908–17921HhPH1_gp283374.3Capsid protein VP3 (ORF28). 91% aa similarity to SH1 VP3 (ORF32, YP_271889) and to NJ7G_2365 of Natrinema sp. J7-2
2917928–18617HhPH1_gp292294.2Capsid protein VP6 (ORF29). 83% aa similarity to SH1 VP6 (ORF33, YP_271890). Also to NJ7G_3194 of Natrinema sp. J7-2 and Hmuk_0476 of Halomicrobium mukohataei. Predicted carboxypeptidase regulatory-like domain (CarboxypepD_reg, pfam13620)
3018614–18943HhPH1_gp301094.971% aa similarity to SH1 ORF34 (YP_271891) and to putative protein 27 of HHIV-2 (AFD02308); Predicted signal sequence (signalP)
3119054–19176cHhPH1_gp31405.0Two CxxC motifs. No homolog in SH1 or HHIV-2
3219173–19289cHhPH1_gp32384.168% aa similarity to SH1 ORF37 (YP_271894)
3319286–19552cHhPH1_gp33885.358% aa similarity to SH1 ORF39 (YP_271896) and to HHIV-2 putative protein 29 (AFD02310). Four CxxC motifs
3419549–19731cHhPH1_gp34607.0Contains CxxC motif. No homolog in SH1 or HHIV-2
3519728–20219cHhPH1_gp351635.693% aa similarity to SH1 ORF 41 (YP_271898) and to putative protein 30 of HHIV-2 (AFD02311)
3620216–21415cHhPH1_gp363995.095% aa similarity to SH1 ORF 42 (YP_271899) and to putative protein 31 of HHIV-2 (AFD02312)
3721419–21778cHhPH1_gp371194.191% aa similarity to SH1 ORF43 (YP_271900) and to putative protein 32 of HHIV-2 (AFD02313)
3821762–23006cHhPH1_gp384144.283% aa similarity to SH1 ORF44 (YP_271901) and to putative protein 33 of HHIV-2 (AFD02314). Predicted coil-coil and helix-turn-helix domains
3923003–23158cHhPH1_gp39516.569% aa similarity to SH1 ORF45 (YP_271902)
4023161–23370cHhPH1_gp40693.574% aa similarity to SH1 ORF46 (YP_271903), and 55% similarity to putative protein 35 of HHIV-2 (AFD02316)
4123422–23586cHhPH1_gp41547.686% aa similarity to SH1 ORF47 (YP_271904); Contains 2 CxxC motifs, and shows similarity to protein domain family PF14206. Arginine-rich
4223583–24023cHhPH1_gp424.877% aa similarity to SH1 ORF48 (YP_271905) and to putative protein 36 of HHIV-2 (AFD02317); Hham1_14540 of Hcc. hamelinensis (ZP_11271999); PhiCh1p72 of Natrialba phage PhiCh1 (NP_665989). DUF4326 (pfam14216) family domain
4324020–24538cHhPH1_gp431724.779% aa similarity to SH1 ORF49 (YP_271906), and 56% similarity to putative protein 37 of HHIV-2 (AFD02318)
4424535–25053cHhPH1_gp441724.392% aa similarity to SH1 ORF50 (YP_271907), and 72% similarity to putative protein 38 of HHIV-2 (AFD02319)
4525050–25277cHhPH1_gp45754.3No homolog in SH1 or HHIV-2.
4625274–25387cHhPH1_gp46374.8No homolog in SH1 or HHIV-2
4725533–25904HhPH1_gp471234.361% aa similarity to SH1 ORF51 (YP_271908); 66% similarity to putative protein 39 of HHIV-2 (AFD02320). Predicted COG1342 domain (DNA binding/helix-turn-helix)
4825901–26092cHhPH1_gp48634.9Contains CxxC motif. No homolog in SH1 or HHIV-2
4926089–27648cHhPH1_gp495064.081% aa similarity to SH1 ORF55 (YP_271912) (but only in the N-terminal half). Homolog of virus structural protein VP18 of HHIV-2 (AFD02323)

ORFs were predicted either by GLIMMER or by manual searching for homologs in the GenBank database.
Start and end positions of ORFs are give in bp number according to the PH1 sequence deposited at GenBank (KC252997). ORFs on the complementary strand are denoted by the suffix c.
Length of the predicted ORF, in number of amino acids.