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 BPHYT_RS11750 BPHYT_RS11750 spermidine/putrescine ABC transporter ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__BFirm:BPHYT_RS11750 Length = 393 Score = 187 bits (476), Expect = 3e-52 Identities = 101/241 (41%), Positives = 146/241 (60%), Gaps = 5/241 (2%) Query: 2 IRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIY 61 I F VSK Y D V+++ LD++ GEF +GPSG GKTTTL M+ T G I Sbjct: 7 ISFSGVSKSY-DGAQYVVDDLNLDVRKGEFLSLLGPSGSGKTTTLMMLAGFESPTHGEIR 65 Query: 62 INEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELLD 121 ++ +R+ D H+ DIG V Q ALFPH+TI EN+A +++ S+ + R+ L+ Sbjct: 66 LDGRRLDDKPPHQR--DIGMVFQNYALFPHLTIAENVAFPLSVRRVSRAEQKKRVQRALE 123 Query: 122 SVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDIS 181 + L +R+PA+LSGG+QQRV + RAL +P ++LMDEP ALD R+ +Q +I Sbjct: 124 MIELP--HLANRRPAQLSGGQQQRVALARALVFEPSVVLMDEPLGALDKRLRETMQYEIM 181 Query: 182 ALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLASG 241 L +++ TIV+VTHD EAL + DR+ V G I Q ATP E+ +N +N FV +F+ Sbjct: 182 RLHRELSLTIVYVTHDQAEALTMSDRVAVFSDGRIQQAATPTELYENAQNAFVANFVGEN 241 Query: 242 H 242 + Sbjct: 242 N 242 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: 295 Number of extensions: 11 Number of successful extensions: 3 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: 393 Length adjustment: 29 Effective length of query: 299 Effective length of database: 364 Effective search space: 108836 Effective search space used: 108836 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