Archaea

Research Article

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

Table 4

ORF annotations of the halovirus PH1 genome.


ORF^a	Position^b	Locus tag	Length^c (aa)	pKi	Similarity/characteristics

1	441–605	HhPH1_gp01	50	4.3	76% aa similarity to SH1 ORF2 (YP_271859)
2	602–802	HhPH1_gp02	66	10.9	80% aa similarity to SH1 ORF3 (YP_271860)
3	802–1059	HhPH1_gp03	85	3.9	85% aa similarity to SH1 ORF4 (YP_271861). 44% similarity to HHIV-2 protein 1
4	1056–1283	HhPH1_gp04	75	3.9	85% aa identity to SH1 ORF5 (YP_271862). Predicted coiled-coil region.
5	1276–1686	HhPH1_gp05	136	4.9	80% 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%)
6	1683–1829	HhPH1_gp06	48	6.1	81% aa similarity to SH1 ORF7 (YP_271864). Predicted signal sequence (SignalP).
7	1822–2130	HhPH1_gp07	102	5.8	91% 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)
8	2123–2383	HhPH1_gp08	86	4.2	90% aa similarity to SH1 ORF9 (YP_271866)
9	2380–2714	HhPH1_gp09	111	5.2	88% 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)
10	2861–3004	HhPH1_gp10	47	10.4	Weak similarity to SH1 ORF12 (YP_271869) only over the N-terminal 18 residues
11	3029–3100	HhPH1_gp11	23	12.3	Not present in SH1 or HHIV-2
12	3134–7453	HhPH1_gp12	1439	4.2	Capsid 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)
13	7505–8227	HhPH1_gp13	240	5.4	Predicted 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)
14	8419–8228c	HhPH1_gp14	63	5.1	43% aa similarity to SH1 ORF18 (YP_271875). Alanine-rich. Central transmembrane domain (Phobius)
15	8856–8416c	HhPH1_gp15	146	4.1	92% 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
16	8853–9500c	HhPH1_gp16	215	3.9	65% 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)
17	9500–9919c	HhPH1_gp17	139	4.1	79% 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)
18	9923–10594c	HhPH1_gp18	223	4.3	83% 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.
19	10659–10943	HhPH1_gp19	94	10.4	Capsid 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)
20	10960–11517	HhPH1_gp20	185	4.4	Capsid 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
21	11519–12217	HhPH1_gp21	232	4.1	Capsid 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
22	12233–12454	HhPH1_gp22	73	3.9	81% aa similarity to SH1 ORF26 (YP_271883) and also to putative protein 17 of HHIV-2 (AFD02298);
23	12458–12697	HhPH1_gp23	79	4.8	78% 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).
24	12701–15064	HhPH1_gp24	787	3.9	Capsid 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).
25	15065–15961	HhPH1_gp25	298	4.5	Putative 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.
26	15964–16446	HhPH1_gp26	160	4.6	73% 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).
27	16446–16895	HhPH1_gp27	149	4.2	Capsid protein VP9 (ORF27). 94% aa similarity to SH1 VP9 (ORF31, YP_271888) and to ZOD2009_19143 of Hap. paucihalophilus (ZP_08046191)
28	16908–17921	HhPH1_gp28	337	4.3	Capsid protein VP3 (ORF28). 91% aa similarity to SH1 VP3 (ORF32, YP_271889) and to NJ7G_2365 of Natrinema sp. J7-2
29	17928–18617	HhPH1_gp29	229	4.2	Capsid 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)
30	18614–18943	HhPH1_gp30	109	4.9	71% aa similarity to SH1 ORF34 (YP_271891) and to putative protein 27 of HHIV-2 (AFD02308); Predicted signal sequence (signalP)
31	19054–19176c	HhPH1_gp31	40	5.0	Two CxxC motifs. No homolog in SH1 or HHIV-2
32	19173–19289c	HhPH1_gp32	38	4.1	68% aa similarity to SH1 ORF37 (YP_271894)
33	19286–19552c	HhPH1_gp33	88	5.3	58% aa similarity to SH1 ORF39 (YP_271896) and to HHIV-2 putative protein 29 (AFD02310). Four CxxC motifs
34	19549–19731c	HhPH1_gp34	60	7.0	Contains CxxC motif. No homolog in SH1 or HHIV-2
35	19728–20219c	HhPH1_gp35	163	5.6	93% aa similarity to SH1 ORF 41 (YP_271898) and to putative protein 30 of HHIV-2 (AFD02311)
36	20216–21415c	HhPH1_gp36	399	5.0	95% aa similarity to SH1 ORF 42 (YP_271899) and to putative protein 31 of HHIV-2 (AFD02312)
37	21419–21778c	HhPH1_gp37	119	4.1	91% aa similarity to SH1 ORF43 (YP_271900) and to putative protein 32 of HHIV-2 (AFD02313)
38	21762–23006c	HhPH1_gp38	414	4.2	83% aa similarity to SH1 ORF44 (YP_271901) and to putative protein 33 of HHIV-2 (AFD02314). Predicted coil-coil and helix-turn-helix domains
39	23003–23158c	HhPH1_gp39	51	6.5	69% aa similarity to SH1 ORF45 (YP_271902)
40	23161–23370c	HhPH1_gp40	69	3.5	74% aa similarity to SH1 ORF46 (YP_271903), and 55% similarity to putative protein 35 of HHIV-2 (AFD02316)
41	23422–23586c	HhPH1_gp41	54	7.6	86% aa similarity to SH1 ORF47 (YP_271904); Contains 2 CxxC motifs, and shows similarity to protein domain family PF14206. Arginine-rich
42	23583–24023c	HhPH1_gp42		4.8	77% 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
43	24020–24538c	HhPH1_gp43	172	4.7	79% aa similarity to SH1 ORF49 (YP_271906), and 56% similarity to putative protein 37 of HHIV-2 (AFD02318)
44	24535–25053c	HhPH1_gp44	172	4.3	92% aa similarity to SH1 ORF50 (YP_271907), and 72% similarity to putative protein 38 of HHIV-2 (AFD02319)
45	25050–25277c	HhPH1_gp45	75	4.3	No homolog in SH1 or HHIV-2.
46	25274–25387c	HhPH1_gp46	37	4.8	No homolog in SH1 or HHIV-2
47	25533–25904	HhPH1_gp47	123	4.3	61% 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)
48	25901–26092c	HhPH1_gp48	63	4.9	Contains CxxC motif. No homolog in SH1 or HHIV-2
49	26089–27648c	HhPH1_gp49	506	4.0	81% 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.