Align BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized)
to candidate AO353_07790 AO353_07790 choline ABC transporter ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__pseudo3_N2E3:AO353_07790 Length = 392 Score = 184 bits (467), Expect = 3e-51 Identities = 111/275 (40%), Positives = 161/275 (58%), Gaps = 32/275 (11%) Query: 1 MIRFDNVSKKYSDDKTAA----------------------VNNVTLDIKDGEFFVFIGPS 38 +IRFDNV +S D A V +LDI+ GE V +G S Sbjct: 3 IIRFDNVDVIFSKDPREALKLLDQGMTRDQILKKTGQIVGVEKASLDIEKGEICVLMGLS 62 Query: 39 GCGKTTTLKMINRLIPLTTGTIYINEKR----ISDYDIHELRW----DIGYVLQQIALFP 90 G GK++ L+ IN L ++ G +++ + I+ EL+ I V Q+ AL P Sbjct: 63 GSGKSSLLRCINGLNTVSRGKLFVEHEGRQIDIASCTPAELKMMRTKRIAMVFQKFALMP 122 Query: 91 HMTIEENIAIVPELKKWSKEKIHDRITELLDSVGLDPESYRHRKPAELSGGEQQRVGVVR 150 +T+ ENI+ E++ +++ + E L+ VGL +R++KP ELSGG QQRVG+ R Sbjct: 123 WLTVRENISFGLEMQGRPEKERRQLVDEKLELVGLT--QWRNKKPDELSGGMQQRVGLAR 180 Query: 151 ALAADPGIILMDEPFSALDPISRQRLQQDISALQKKIKKTIVFVTHDMQEALALGDRICV 210 ALA D I+LMDEPFSALDP+ RQ LQ ++ LQ+K+ KTIVFV+HD+ EAL LG RI + Sbjct: 181 ALAMDADILLMDEPFSALDPLIRQGLQDELLELQRKLHKTIVFVSHDLDEALKLGSRIAI 240 Query: 211 MQGGEIVQVATPQEIMKNPENDFVKDFLASGHAFN 245 M+ G I+Q + P+EI+ NP +D+V+ F+A + N Sbjct: 241 MKDGRIIQYSKPEEIVLNPADDYVRTFVAHTNPLN 275 Lambda K H 0.318 0.136 0.386 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 302 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 328 Length of database: 392 Length adjustment: 29 Effective length of query: 299 Effective length of database: 363 Effective search space: 108537 Effective search space used: 108537 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory