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 Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 164 bits (415), Expect = 3e-45 Identities = 91/251 (36%), Positives = 147/251 (58%), Gaps = 10/251 (3%) Query: 2 IRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIY 61 I N++K++ + A+++V+L I GE +GPSGCGKTT L++I + G + Sbjct: 3 IEIRNIAKRFGN--FVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVM 60 Query: 62 INEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIA----IVPELKKWSKEKIHDRIT 117 + +H +G+V Q ALF HM + EN+A + P ++ + +I R+ Sbjct: 61 FEGSEATH--LHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVM 118 Query: 118 ELLDSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQ 177 +LL V LD + R+ P +LSGG++QR+ + RALA +P ++L+DEPF ALD R+ L+ Sbjct: 119 DLLSLVQLDWLADRY--PTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELR 176 Query: 178 QDISALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDF 237 + + L ++ + VFVTHD +EAL + DR+ VM G I QV +P E+ NP + FV F Sbjct: 177 RWLRRLHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQF 236 Query: 238 LASGHAFNTPI 248 L + + F++ + Sbjct: 237 LGNVNVFHSRV 247 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: 254 Number of extensions: 9 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: 360 Length adjustment: 29 Effective length of query: 299 Effective length of database: 331 Effective search space: 98969 Effective search space used: 98969 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 Apr 09 2024. 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