Align BilEB aka OpuBB 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_022528965.1 L248_RS04780 ABC transporter permease/substrate-binding protein
Query= TCDB::Q93A34 (504 letters) >NCBI__GCF_000469325.1:WP_022528965.1 Length = 507 Score = 528 bits (1361), Expect = e-154 Identities = 277/508 (54%), Positives = 367/508 (72%), Gaps = 13/508 (2%) Query: 4 LIDTFTVRKDELFTALVQHIQISFVSLFIAVLIALPLGIYLTRHKRLAEPIIQVAAIFQT 63 +I T R+ +L +AL QH+ IS ++L IA++IA+PL + RH + A ++Q+A I QT Sbjct: 3 IISTLVDRRQQLLSALGQHLSISLIALVIAIIIAMPLAFWAARHSKAAAVLLQIAGILQT 62 Query: 64 IPSLALLGLLIPLVGIGIVPAIIALVIYALLPILRNTYTGIKEVDPALVEASRAMGMNKW 123 IPSLALLGLLIPLVGIG PA+IALVIYALLPI +NTY GI +DPAL EA+ A GM +W Sbjct: 63 IPSLALLGLLIPLVGIGTTPAVIALVIYALLPIFQNTYIGITGIDPALEEAADAFGMGRW 122 Query: 124 KRLYKVQLPLAMPVIMAGIRTAMVLIIGTATLAALIGAGGLGDLILLGIDRNDNSLILLG 183 ++L KV+LPLA P I+ GIRTA+VLIIGTATLAALIGAGGLG ILLGIDRN+ +LI++G Sbjct: 123 RKLRKVELPLAAPTIIGGIRTALVLIIGTATLAALIGAGGLGSFILLGIDRNNTALIVIG 182 Query: 184 AIPAALLAILFDFLLRFLEKASFKSTIITISAGILLTAAIIV----VPYFASDKKEITVA 239 A+ +ALLAI+ L+ +L K ++ T AG+++ + V + + + + +A Sbjct: 183 AVFSALLAIILSALISWLAKQRWQWT-----AGLVVLLILGVGGTQIASRVNQPETVVIA 237 Query: 240 GKLGAEPEILINMYKLVIE-DETDLKVNVKPNMGKTSFVFNALKSGDIDIYPEFTGTVLE 298 GKLG+EP+ILINMYK +IE D+ ++V +K N GKT+F+FNA+K+G +DIYPEFTGTVLE Sbjct: 238 GKLGSEPDILINMYKQLIEHDDPHIRVQLKSNFGKTTFLFNAVKTGSVDIYPEFTGTVLE 297 Query: 299 TFLKEN--AKTHDPEEVYTQARDGLAKDFDMTYLKPMKYNNTYALAVSPEFAKENNLEKI 356 T +K++ A + YT AR L+K F MTYL+PM Y NTY +AV FA+++ L I Sbjct: 298 TLVKQDRTAAHLTAAQTYTAARQALSKQFQMTYLQPMAYQNTYGVAVKRRFAQDHGLTTI 357 Query: 357 SDLGPVSDQVKAGFTLEFKDRSDGYKGIQDKYGLTFSNLKTMEPKLRYNAIKSGDINLLD 416 S L V+DQ+ AGFTLEF DR DGY+G++ YGL F + EP LRY AI +G +NL+D Sbjct: 358 SSLRNVTDQLSAGFTLEFLDRPDGYQGLKKVYGLHFPT-HSFEPALRYAAINNGKVNLVD 416 Query: 417 AYSTDSELAQYKLKVLEDDQQLFPPYQGAPLMLTKTLDKYPELKKPLNKLAGKITDDEMR 476 YSTDSE+ QYKL+VL DD+ LFPPYQGAPLM T ++P + + LNKLAG ITD +M+ Sbjct: 417 VYSTDSEIVQYKLQVLRDDKHLFPPYQGAPLMRTAFARQHPGIVRSLNKLAGHITDKQMQ 476 Query: 477 KMNYEVNVNGKSAYTVAKDYLKDQGIIK 504 +MNY VNV +S VA+ YL G++K Sbjct: 477 QMNYAVNVRNESPAKVARTYLTSHGLLK 504 Lambda K H 0.320 0.139 0.387 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: 581 Number of extensions: 19 Number of successful extensions: 5 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: 504 Length of database: 507 Length adjustment: 34 Effective length of query: 470 Effective length of database: 473 Effective search space: 222310 Effective search space used: 222310 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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