. Author manuscript; available in PMC: 2008 Nov 25.

Published in final edited form as: Virology. 2007 Jul 30;368(2):405–421. doi: 10.1016/j.virol.2007.06.043

Table 1.

Identifying information of 0305φ8-36 gene products.

Gp	aa	Identifying information¹	Homologues²
Gp	aa	Identifying information¹	Organism, protein identifier (% identity, E value from Psi-Blast) or (method used to detect homologue)	Paralogues
112	242		B. thuringiensis RBTH_06519 (40% over 116, 9e-15)
113	194	STR.
114	248	STR.
116	181	STR.
117	635	terminase, large subunit	B. thuringiensis RBTH_06375 (31% over 570, 1e-58)
118	428	STR.
119	401	MAJOR STR., putative curly fiber
121	100	3 predicted transmembrane helices
122	648	STR., portal	B. thuringiensis RBTH_06377 (43% over 465, 1e-102) Halovirus HF1 GI:32346486 (23% over 320, 1e-07)
123	487	protease (SAM) with nested scaffold (gp123*, 257 aa)	B. thuringiensis RBTH_06378 (27% over 406, 2e-29)
124	364	MAJOR STR., head decoration	B. thuringiensis RBTH_06380 (27% over 420, 7e-16)
125	393	MAJOR STR, HK97-like major capsid	B. thuringiensis RBTH_06381 (40% over 334, 1e-69)
127	331	STR.
128	143	STR.
129	989	MAJOR STR., putative curly fiber	Clostridium tetani GI:28210805 (41% over 131, 5e-18)
130	1073	STR.
131	119	MAJOR STR., putative curly fiber
132	369	STR.
133	900	STR.		gp152, gp154, gp155, gp135
134	123	STR.		gp157
135	288	STR.		gp155, gp133, gp154, gp152
136	177	STR.
137	529	STR.	B. thuringiensis RBTH_08838 (26% over 164, 7e-05)	gp139
138	226	STR.	B. thuringiensis RBTH_06388 (31% over 196, 7e-14)
139	717	MAJOR STR., tail sheath	B. thuringiensis RBTH_08838 (29% over 269, 5e-23)	gp137
140	260	MAJOR STR., putative tail tube	B. thuringiensis RBTH_07699 (34% over 232, 3e-25)	gp141
141	502	STR.	B. thuringiensis RBTH_07698 (39% over 151, 8e-23)	gp140
142	558	STR.	B. thuringiensis RBTH_07697 (40% over 111, 3e-14)	gp209
143	218		B. thuringiensis RBTH_07696 (40% over 114, 6e-16)	gp144
144	262		B. thuringiensis RBTH_07695 (29% over 158, 7e-11)	gp143
145	1930	STR.	B. thuringiensis RBTH_07694 (32% over 673, 9e-86)
146	2536	STR., putative tape measure
147	1903	T4 gp27, baseplate hub-like (SAM)	B. thuringiensis RBTH_07688 (28% over 515, 2e-40)
148	127	putative baseplate assembly	P2 gpV-like (SAM), Mu gp45-like (SAM)
149	187		B. thuringiensis RBTH_07683
150	141		B. thuringiensis RBTH_07682 (40% over 95, 1e-08)
151	270	STR., P2 gpJ-like baseplate	B. thuringiensis RBTH_07681 (33% over 261, 1e-31)
152	265	STR.		gp133, gp154, gp155, gp135, gp197
153	383	STR.
154	1212	STR., beta glucosidase³ (R-Psi)	Saccharophagus degradans 2–40 GI:90020793 (30% over 107, 0.025)	gp152, gp155, gp133, gp135, gp197
155	936	STR.		gp154, gp133, gp152, gp135
156	204	STR.
157	127	STR.		gp134
158	293	STR.		gp159, gp160
159	270	STR.		gp158, gp160
160	267	STR.		gp158, gp159
161	114	STR.
162	372	STR.³	B. thuringiensis RBTH_07680 (33% over 212, 7e-21)
163	2143	STR., 4 x FN3	Mus musculus GI:90403603 (24% over 390, 6e-10)
164	1062	STR., Von Willebrand’s domain	B. thuringiensis RBTH_07673 (33% over 238, 1e-29); RBTH_08837 (26% over 250, 3e-10)
165	421	STR., 3 x FN3		gp166
166	406	STR., 3 x FN3		gp165
167	591	STR., 4 x FN3	B. cereus GI:29896472 (28% over 198, 5e-11)	gp199
168	693	STR.
171	755	STR.	B. thuringiensis RBTH_07661 (26% over 389, 1e-23); RBTH_07663 (22% over 246, 1e-04); RBTH_07662 (25% over 90, 0.29)
172	591	STR.	B. thuringiensis RBTH_07660 (22% over 565, 6e-15)
173	686	STR.	B. thuringiensis RBTH_07659 (20% over 614, 3e-17)
174	82	STR.
175	398	STR.	B. thuringiensis RBTH_07657 (25% over 221, 1e-09)
180	229		B. thuringiensis RBTH_07119 (33% over 150, 7e-16)
181	316	Archaeal primase	B. thuringiensis RBTH_07120 (31% over 291, 1e-40)
182	346	dnaB helicase	B. thuringiensis RBTH_07121 (42% over 323, 1e-69)
190	269	RecB	B. thuringiensis RBTH_07113 (26% over 273, 4e-24)
192	177	RuvC, Holliday junction resolvase	Caldicellulosiruptor saccharolyticus GI:82501051 (28% over 169, 1e-05)
193	287		C. acetobutylicum, GI:15004860 (23% over 263, 1e-12)
194	170	homing nuclease	Invertebrate iridescent virus 6, GI:15079019 (40% over 84, 1e-09)
196	185	thymidine kinase	Bacillus sp. GI:89095598 (41% over 177, 2e-30)
197	78	STR.³
198	135	STR., FN3	cd00063, FN3 (24% over 85, 2e-04)	gp167
199	486	STR., 4X FN3	Solibacter usitatus GI:67929848 (40% over 92, 2e-08)
201	802		Silicibacter pomeroyi GI:56677853 (22% over 310, 2e-09)
205	171	STR.
207	330	mreB-like rod determination protein	Symbiobacterium thermophilum GI:51858110 (25% over336, 1e-16)
208	143	transcription factor	C. acetobutylicum GI:15023852 (35% over 111, 7e-08)
209	585	STR.	B. licheniformis GI:52349990 (30% over 245, 2e-22)	gp142
210	220	HsdM	COG0286 (20% over 174, 8e-05)
213	139	homing nuclease	phiKZ ORF296 GI:29135232 (51% over 54, 2e-04)
215	255	dCMP deamidase	Lactobacillus gasseri GI:23003434 (62% over 122, 2e-39)
223	159	Flavodoxin	Exiguobacterium sibiricum GI:68056239 (37% over 124, 2e-17)
224	352	nrd beta subunit	E. sibiricum GI:68056370 (46% over 344, 2e-82)
225	767	nrd alpha subunit	Geobacillus kaustophilus GI:56379288 (51% over 774, 0)
227	206		B. thuringiensis RBTH_07176 (40% over 123, 1e-14)
228	179		B. thuringiensis RBTH_07176 (23% over 152, 0.025)
232	145	membrane-bound metal-dependent hydrolase	Desulfotomaculum reducens GI:88944587 (31% over 129, 2e-07)
234	155	COG3236	Escherichia coli GI:16128766 (41% over 153, 3e-29)
236	424	dnaG primase	Prosthecochloris vibrioformis GI:71481478 (29% over365, 2e-33)
237	368	lysin	B. cereus GI:89199806 (68% over 197, 3e-76)
5	236		B. halodurans GI:10174999 (42% over 184, 1e-31)
8	769	rec. exo	C. thermocellum GI:67876361 (28% over 492, 4e-49)
9	182		Mesorhizobium sp. GI:68190552 (42% over 71, 2e-07)	gp10
10	244		B. thuringiensis RBTH_02290 (35% over 128, 1e-08)	gp9
15	250	serine/threonine phosphatase	Lactococcus lactis GI:76574849 (30% over 221, 7e-17)
16	117	MazG	Mx8, p26 GI:15320596 (52% over 113, 9e-21)
23	657	PcrA helicase	Moorella thermoacetica GI:83590844 (42% over 642, 1e-141)
241	457	recA (nb. in two segments as gene interrupted by orf29)	Mycobacterium peregrinum (33% over 374, 3e-46)
29	266	mobile intron	M. vanbaalenii GI:90205066 (35% over 53, 0.004)
33	111	DNA-binding protein HU	B. cereus GI:29895202 (77% over 90, 1e-26)
240	1348	DNA polymerase III alpha subunit (nb. in two segments as gene interrupted by orf36)	C. thermocellum GI:67873315 (30% over 1296, 4e-157)
36	261	mobile intron	B. anthracis GI:47503129, (30% over 214, 8e-15)
239	176	mobile nuclease	Cyanophage P-SSM2, GI:61806163 (35% over 80, 1e-08)
39	361	DNA polymerase III beta subunit	C. perfringens GI:18143659 (28% over 311, 2e-23)
41	104	GroES	Anabaena variabilis GI:75705561 (41% over 92, 3e-12)
43	207	Uracil-DNA glycosylase	Thermoanaerobacter tengcongensis GI:20515053 (30% over 155, 2e-10)
44	352	C-terminal region of bacteriolytic enzyme	B. clausii GI:38603523 (26% over 224, 3e-05)
46	318		N. farcinica GI:54019290 (25% over 330, 1e-14)
53	166	HTH type 11 transcriptional regulator	Vibrio vulnificus GI:37200665 (37% o over 69, 6e-04)
61	248	B. cereus phage phBC6A51,	phBC6A51 GI:31415774 (37% over 79, 2e-06)	gp88
62	235	enterotoxin/cell-wall binding protein	B. cereus GI:42784405 (69% over 110, 1e-37)
63	553	metalloprotein chaperonin subunit	N. farcinica GI:54019291 (27% over 528, 2e-33)
66	471	metalloprotein chaperonin subunit	Listeria monocytogenes GI:47092621 (38% over 288, 2e-43)
70	624	RecQ helicase	B. thuringiensis RBTH_07170 (26% over 624, 5e-52)
79	577	RecJ	B. halodurans GI:10173856 (34% over 562, 8e-95)
81	85	MAJOR STR.
88	154	B. cereus phage phBC6A51	phBC6A51 GI:31415774 (44% over 74, 9e-09)	gp61
97	188		B. thuringiensis RBTH_06730 (34% over 167, 6e-23)
99	1245	putative RNA polymerase	Arabidopsis thaliana GI:24935275 (23% over 475, 2e-04)

Putative functions were assigned based on homologies to proteins detected using Psi-Blast, unless stated otherwise.

Closest homologues detected by Psi-Blast are listed with other matches included, where pertinent. The organism and protein global identifier for homologues are provided, except for B. thuringiensis homologues for which the protein identifiers, beginning RBTH_, are given. B. thuringiensis refers to Bacillus thuringiensis serovar israelensis ATCC 35646. The Psi-Blast matches of 0305φ8-36 proteins to B. thuringiensis or B. weihenstephanensis homologues were very similar. Only the results for the B. thuringiensis homologues are included in this table. Several 0305φ8-36 proteins had more than one B. thuringiensis homologue, in which instance protein identifiers of the additional homologues are included in parenthesis. 0305φ8-36 paralogues are listed.

, single peptide detected by mass spectrometry with decreased confidence (see Table S1).

Abbreviations used: aa, amino acids; FN3, Fibronectin type 3 domain; MAJOR STR., one of the eight most densely stained bands as detected by SDS-PAGE (Figure 2), copy number for each protein was estimated to be >100 copies per virion; SAM, homologous relationship determined using a SAM model; STR., virion structural protein identified by mass spectrometry with a protein identification probability of 98% or greater, unless noted (see Table S1).