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 GFF1013 HP15_991 substrate-binding region of ABC-type glycine betaine transport system
Query= TCDB::Q93A34 (504 letters) >FitnessBrowser__Marino:GFF1013 Length = 305 Score = 128 bits (321), Expect = 3e-34 Identities = 83/275 (30%), Positives = 142/275 (51%), Gaps = 16/275 (5%) Query: 236 ITVAGKLGAEPEILINMYKLVIEDETDLKVNVKPNMGKTSFVFNALKSGDIDIYPEFTGT 295 + V+ K+ E +L M +E + V + +G TS V NA+K+G+IDIYPE+TG Sbjct: 28 VVVSSKIDTEGSVLGQMVLQSLEG-AGIPVENRLQLGGTSIVRNAIKAGEIDIYPEYTGN 86 Query: 296 VLETFLKENAKTH---DPEEVYTQARDGLAKDFDMTYLKPMKYNNTYALAVSPEFAKENN 352 F + A D ++ Y +A + ++ +L+P + NNT+A++V + A+ENN Sbjct: 87 A--AFFHDQADLDIWKDADKAYQEAARLDKEAHNIVWLEPAEANNTWAMSVRGDLARENN 144 Query: 353 LEKISDLGPVSDQ---VKAGFTLEFKDRSDGYKGIQDKYGLTFSNLKTM-------EPKL 402 L + DL ++ K + EF + + Q+ YG + + + L Sbjct: 145 LATLEDLADYINEGGAFKFAASAEFVESASALPAFQEAYGFKLESDQLLILSGGNTAATL 204 Query: 403 RYNAIKSGDINLLDAYSTDSELAQYKLKVLEDDQQLFPPYQGAPLMLTKTLDKYPELKKP 462 R A+ + D+N Y TD L LKV+ED + P YQ AP++ + L+ YP++++ Sbjct: 205 RAAALNNNDVNGAMTYGTDGGLDALDLKVMEDTAGVQPVYQPAPIVRGEVLEAYPQIREV 264 Query: 463 LNKLAGKITDDEMRKMNYEVNVNGKSAYTVAKDYL 497 L + + + ++++N +V VNG A TVA+DYL Sbjct: 265 LTPIFESLDLETLQRLNGQVAVNGVPADTVARDYL 299 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: 279 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: 504 Length of database: 305 Length adjustment: 31 Effective length of query: 473 Effective length of database: 274 Effective search space: 129602 Effective search space used: 129602 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: 50 (23.9 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