Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate RR42_RS04400 RR42_RS04400 ABC transporter permease
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__Cup4G11:RR42_RS04400 Length = 219 Score = 100 bits (248), Expect = 6e-26 Identities = 63/208 (30%), Positives = 117/208 (56%), Gaps = 15/208 (7%) Query: 226 GFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLL 285 G LL + + +++ L LG ++AL S + K+++ + +RG PL+ +F + Sbjct: 17 GMLLTIKFALLSMIFGLVLGTVVALMGISHQPVPKAVARAYVSIMRGTPLLVQIF----V 72 Query: 286 LQYFLPP-GTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQ 344 + Y LP G + V+ ++L AY++E +RG + +PRGQ+ AA +LGL QA Sbjct: 73 VYYGLPGIGIALEPTPAGVLTLSLNVGAYLSESMRGAILGIPRGQWLAAYSLGLTQGQAL 132 Query: 345 RLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEP- 403 R +I PQAL++++P + +S I L KDT+LV+ + + + L+ V+ + ++P Sbjct: 133 RYVIGPQALRLAVPSLSNSLISLIKDTSLVSVITVTELLRTAQEVIAAT-------YQPL 185 Query: 404 --YIFVALIFFLFNFSMSRYSMYLERKL 429 Y+ VA I+++ + +++ LER+L Sbjct: 186 PLYLAVAAIYWMLSTALAHMQRLLERRL 213 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: 251 Number of extensions: 12 Number of successful extensions: 1 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: 219 Length adjustment: 27 Effective length of query: 407 Effective length of database: 192 Effective search space: 78144 Effective search space used: 78144 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