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 WP_057508907.1 ABB28_RS12160 methionine ABC transporter ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >NCBI__GCF_001431535.1:WP_057508907.1 Length = 335 Score = 144 bits (364), Expect = 2e-39 Identities = 93/281 (33%), Positives = 150/281 (53%), Gaps = 8/281 (2%) Query: 1 MIRFDNVSKKYSDDKTA--AVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTG 58 MI F + K Y+ A A+ + L I++GE F IG SG GK+T ++MINRL + G Sbjct: 1 MIEFQRLHKSYAVAGRAISALQPLDLTIQEGEVFGIIGHSGAGKSTLIRMINRLEDPSGG 60 Query: 59 TIYINEKRISDYD---IHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDR 115 + I + ++ + + LR IG + Q L T+ N+A EL + +I R Sbjct: 61 RLLIAGEDVTALETAGLRTLRRRIGMIFQHFNLLSSRTVASNVAFPLELAGTPRAQIDAR 120 Query: 116 ITELLDSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQR 175 + ELL +VGL +++ + PA+LSGG++QRVG+ RALA P I+L DE SALDP + Sbjct: 121 VAELLQTVGL--QAHADKYPAQLSGGQKQRVGIARALATGPQILLCDEATSALDPQTTAS 178 Query: 176 LQQDISALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVK 235 + +S + +++ TIV +TH+M + DR+ V+ GE+V++ ++ +P++ + Sbjct: 179 VLALLSKINRELGLTIVLITHEMDVIRRVCDRVAVLDAGEMVEMGPVTDVFLHPQHPTTR 238 Query: 236 DFLASGHAFNTPILEANF-TVNDLIEADLFYSYQTSDGTLG 275 F++ + L +F TV I F T LG Sbjct: 239 RFVSESEHIDEGTLHGDFDTVGGTIVRLTFLGADTYQPLLG 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: 248 Number of extensions: 12 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: 335 Length adjustment: 28 Effective length of query: 300 Effective length of database: 307 Effective search space: 92100 Effective search space used: 92100 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 24 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