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 SM_b21146 SM_b21146 choline uptake ABC transporter ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__Smeli:SM_b21146 Length = 312 Score = 223 bits (569), Expect = 4e-63 Identities = 125/261 (47%), Positives = 162/261 (62%), Gaps = 6/261 (2%) Query: 1 MIRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTI 60 MI + +SK+Y D T V++V+L + V +G SG GKTT L+MINRL+ T GTI Sbjct: 1 MIEIEEISKRYGD--TTVVSDVSLTVAPHTVTVVVGTSGSGKTTLLRMINRLVEPTAGTI 58 Query: 61 YINEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELL 120 I+ + ELR IGY +Q LFPH T+ +NIA VP L W K +I ++ ELL Sbjct: 59 KIDGEDNRSIPGFELRRRIGYAIQGHGLFPHRTVAQNIATVPTLLGWEKARIDAKVEELL 118 Query: 121 DSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDI 180 LDP + R P ELSGG+QQRVGV RALAA+P ++LMDEPF ALDPI R + Q D+ Sbjct: 119 KLFQLDPSEFGPRYPHELSGGQQQRVGVARALAAEPNVLLMDEPFGALDPIIRAKAQDDL 178 Query: 181 SALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFL-A 239 +A+QK TI+ VTHDM+EA L DRI VM GE+VQ ATP E++ P FV+ + A Sbjct: 179 AAIQKHFGTTIILVTHDMEEAFHLADRIAVMDKGEVVQYATPAEMLVRPATPFVETLVGA 238 Query: 240 SGHAFNTPILEANFTVNDLIE 260 S F +E TV + +E Sbjct: 239 SERPFRLLDIE---TVGEAVE 256 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: 241 Number of extensions: 7 Number of successful extensions: 1 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: 312 Length adjustment: 28 Effective length of query: 300 Effective length of database: 284 Effective search space: 85200 Effective search space used: 85200 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: 48 (23.1 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