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 Ac3H11_909 Sulfate and thiosulfate import ATP-binding protein CysA (EC 3.6.3.25)
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_909 Length = 374 Score = 175 bits (444), Expect = 1e-48 Identities = 97/248 (39%), Positives = 154/248 (62%), Gaps = 10/248 (4%) Query: 2 IRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIY 61 I NVSK++ D + A+ +V+LDI+ GE +GPSGCGKTT L++I L GTI+ Sbjct: 3 IEIRNVSKQFGDFQ--ALRDVSLDIQSGELIALLGPSGCGKTTLLRIIAGLETADVGTIH 60 Query: 62 INEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIA----IVPELKKWSKEKIHDRIT 117 + + +D + E ++G+V Q ALF HMT+ EN+A + P ++ S+ +I ++ Sbjct: 61 FSGEDTTDVHVRER--NVGFVFQHYALFRHMTVFENVAFGLRVKPRSERPSEAQIKKKVM 118 Query: 118 ELLDSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQ 177 +LL V LD + R+ P++LSGG++QR+ + RALA +P ++L+DEPF ALD R+ L+ Sbjct: 119 DLLKLVQLDWLAERY--PSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELR 176 Query: 178 QDISALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDF 237 + + L ++ T +FVTHD +EAL + DR+ V+ G I Q +PQ++ P + FV F Sbjct: 177 RWLRRLHDELHVTSIFVTHDQEEALEVADRVVVINQGRIEQSGSPQQVWDQPASPFVYGF 236 Query: 238 LASGHAFN 245 L + F+ Sbjct: 237 LGDVNLFH 244 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: 274 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: 374 Length adjustment: 29 Effective length of query: 299 Effective length of database: 345 Effective search space: 103155 Effective search space used: 103155 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