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 Pf6N2E2_240 L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1)
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_240 Length = 296 Score = 199 bits (507), Expect = 5e-56 Identities = 114/280 (40%), Positives = 164/280 (58%), Gaps = 19/280 (6%) Query: 48 MINRLIPLTTGTIYINEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKW 107 MINRL +G I +N + D+ LR IG+++Q ALFPH T+ ENI VP L W Sbjct: 1 MINRLDTQDSGRISVNGVATDELDVVTLRRGIGFMMQSSALFPHQTVAENIGAVPRLLGW 60 Query: 108 SKEKIHDRITELLDSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSA 167 SK KI R++EL+ VGL PE + R P +LSGG+Q RV + RALA+DP ++LMDEPF+A Sbjct: 61 SKHKIRQRVSELISLVGLQPE-FLDRYPNQLSGGQQSRVALARALASDPPVVLMDEPFAA 119 Query: 168 LDPISRQRLQQDISALQKKIKKTIVFVTHDMQEALALGDRICVMQG-GEIVQVATPQEIM 226 LDP+ R+RLQ ++ ALQ+++ KTI+ VTHDM+EA+ +GDRI + +G G++ Q TP I+ Sbjct: 120 LDPVIRERLQDELVALQRRLHKTIILVTHDMEEAIKIGDRIAIFEGEGKLAQFDTPHNIL 179 Query: 227 KNPENDFVKDFLASG---------HAFNTPILEANFTVNDLIEADLFYSYQTSDGTLGIS 277 +P ++FVK+F+ + P+ E N L++ S+ L + Sbjct: 180 AHPASEFVKNFIGKDPLLKRLSLMKVSDLPVDEVNCEFKLLLDDKSNPLKWVSESDLPVP 239 Query: 278 STEPVEN-------LVRRIAEEQSIPV-TDEAGNYIGTVS 309 V N LV+ + + V DEAG Y G +S Sbjct: 240 ELTTVSNNDSLHHALVKILTAPLGVVVRVDEAGGYEGCLS 279 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: 246 Number of extensions: 8 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: 296 Length adjustment: 27 Effective length of query: 301 Effective length of database: 269 Effective search space: 80969 Effective search space used: 80969 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