The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization

Table 3 Search for trpD and trpA genes using multiple probes

Species and strain*	matches†	both‡	probe only§	Bacillus only¶	% new¥
*trpD*
Sulfolobus solfataricus P2	454	444	10	24	2
Thermoplasma acidophilum DSM 1728	409	404	5	64	1
Nostoc sp. PCC 7120	436	430	6	38	1
Thermoanaerobacter tengcongensis MB4	493	467	26	1	6
Rhodopirellula baltica SH 1	448	442	6	26	1
Bacteroides fragilis NCTC 9343	424	419	5	49	1
Corynebacterium jeikeium K411	443	433	10	35	2
Methanosphaera stadtmanae DSM 3091	441	433	8	35	2
Neisseria meningitidis FAM18	474	458	16	10	3
Clostridium kluyveri DSM 555	492	464	28	4	6
All#	514	468	46	0	10
*trpA*
Sulfolobus solfataricus P2	222	222	0	241	0
Nostoc sp. PCC 7120	471	445	26	18	6
Pseudomonas putida KT2440	498	457	41	6	9
Rhodopirellula baltica SH1	478	456	22	7	5
Corynebacterium jeikeium K4111	463	432	31	31	7
Bacteroides fragilis NCTC 9343	437	431	6	32	1
Clostridium kluyveri DSM 555	475	443	32	20	7
Thermoplasma acidophilum DSM 1728	25	25	0	438	0
Neisseria meningitidis 053442	479	452	27	11	6
Leptospira biflexa serovar Patoc	474	451	23	12	5
All#	517	463	54	0	12

* Species and strain, those used to probe the database † Matches, number of genes detected using the specific probe ‡ Both, genes detected by both the specific probe and that from Bacillus; § Probe only, those sequences detected by the specific probe but not by that from Bacillus ¶ Bacillus only, those sequences detected by the Bacillus probe but not by the specific probe ¥ % new, per cent of new sequences not detected by the Bacillus probe # All, the total number of sequences found by all probes; those that were common to Bacillus and one or more of the specific probes; the number of genes found with specific probes but not by that from Bacillus (new sequences); those found by the Bacillus probe but not by the others; the per cent of new sequences, that is the number of new sequences divided by the number of Bacillus sequences times 100. The data given in the table are raw data without the elimination of sequences that are somewhat doubtful because in this table we are trying to maximally expand the search parameters.

ISSN: 1474-760X