Molecular modeling and characterization of Vibrio cholerae transcription regulator HlyU

BMC Structural Biology

Table 1 Proteins found with BLAST search producing alignments (E value ≤ 1 × 10^-20) with the sequence of HlyU from V. cholerae are shown together with proteins with known 3D structure

Genebank code	Protein description	Organism	Score (bits)	E	Sequence identity (%)
ZP_00992718.1	Transcription activator HlyU	Vibrio splendidus	137	2 × 10^-31	82
ZP_01065735.1	Transcription activator HlyU	Vibrio sp.	135	4 × 10^-31	82
NP_759503.1	Transcription activator HlyU	Vibrio vulnificus	132	6 × 10^-30	82
NP_796908.1	Transcription activator HlyU	Vibrio parahaemolyticus	130	2 × 10^-29	83
ZP_01261951.1	Transcription activator HlyU	Vibrio alginolyticus	129	5 × 10^-29	83
ZP_00761653.1	Predicted transcriptional regulator	Vibrio sp.	129	6 × 10^-29	83
YP_128811.1	Putative transcription activator HlyU	Photobacterium profundum	126	3 × 10^-28	75
YP_203846.1	Transcription activator HlyU	Vibrio fischeri	124	2 × 10^-27	73
NP_719085.1	Transcription activator HlyU	Shewanella oneidensis	109	4 × 10^-23	64
YP_751572.1	Transcriptional regulator, ArsR family protein	Shewanella frigidimarina	107	1 × 10^-22	63
ZP_01437145.1	Transcriptional regulator, ArsR family protein	Shewanella baltica	106	2 × 10^-22	63
ZP_00838999.1	Regulatory protein, ArsR	Shewanella sp.	105	5 × 10^-22	63
YP_563729.1	Regulatory protein, ArsR	Shewanella denitrificans	105	5 × 10^-22	63
ZP_01305695.1	Transcription activator HlyU	Oceanobacter sp.	101	1 × 10^-20	58
Proteins with known 3D structure^a
PDB code: 1u2w	Cadmium efflux system accessory protein CadC	Staphylococcus aureus	46.2	2 × 10^-06	34
PDB code: 1r1u	Repressor protein CzrA^b	Staphylococcus aureus	45.4	3 × 10^-06	33
PDB code: 1smt	Transcriptional repressor SmtB^b	Synechococcus sp.	36.2	0.002	37

^a Found from a BLAST search on PDB.
^b A few other closely related structures have PDB codes 1r1v and (1r22, 1r23 and 1r1t).

ISSN: 1472-6807