Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate BWI76_RS18355 BWI76_RS18355 amino acid ABC transporter permease
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__Koxy:BWI76_RS18355 Length = 222 Score = 107 bits (268), Expect = 3e-28 Identities = 71/219 (32%), Positives = 116/219 (52%), Gaps = 11/219 (5%) Query: 219 VDSDQF--GGFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLI 276 +DS F G + L + + + L LG +LAL R S + +K L+ I RG PLI Sbjct: 9 IDSAPFLLKGAVFTLQLSIGGMFFGLVLGFILALMRMSPVWPIKWLARMYISIFRGTPLI 68 Query: 277 TLLFTASLLLQYFLPP-GTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADA 335 LF ++ Y LP G D I +I ++L AAY AE +R +A++ +GQ+EAA + Sbjct: 69 AQLF----MIYYGLPQFGIELDPIPAAMIGLSLNTAAYAAETLRAAIASIDKGQWEAAAS 124 Query: 336 LGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMA 395 +G+ WQA R I+PQA ++++P + +SFI L KDT+L A + + + + + + Sbjct: 125 IGMTRWQAMRRAILPQAARVALPPLSNSFISLVKDTSLAATIQVPELFRQAQLITSRTL- 183 Query: 396 WKGTYWEPYIFVALIFFLFNFSMSRYSMYLERKLKRDHR 434 + Y+ +LI+++ +S Y E +L R R Sbjct: 184 ---EVFTMYLAASLIYWVMATVLSTLQNYFENQLNRQER 219 Lambda K H 0.329 0.143 0.457 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: 259 Number of extensions: 14 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: 434 Length of database: 222 Length adjustment: 27 Effective length of query: 407 Effective length of database: 195 Effective search space: 79365 Effective search space used: 79365 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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