Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate PfGW456L13_3607 Amino acid ABC transporter, permease protein
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3607 Length = 281 Score = 81.6 bits (200), Expect = 3e-20 Identities = 63/203 (31%), Positives = 101/203 (49%), Gaps = 9/203 (4%) Query: 226 GFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASL- 284 G L L + +I +SL LG + AL R S + ++ F RG PL+ + L Sbjct: 77 GAALTLFLCFCSIWLSLLLGFVTALARLSRSAVAFGVASFYASFFRGTPLLIQILLIYLG 136 Query: 285 LLQYFLPPGTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQ 344 L Q + PG I +I ++L AY++E+ R G+ A+ GQ EAA ALGL Sbjct: 137 LPQLGVVPGA----ISAGIIALSLNYGAYLSEIFRAGIMAVAPGQREAAMALGLGPVATF 192 Query: 345 RLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEPY 404 I++PQA++ IP S FI + KD++L++ +G+++ + + RS Y E Sbjct: 193 LHIVLPQAMRTIIPPTTSQFISMLKDSSLISVMGVWEVMFLAQSYGRSSY----RYIEML 248 Query: 405 IFVALIFFLFNFSMSRYSMYLER 427 A+I++L + + LER Sbjct: 249 TTAAVIYWLLSIGLELIQNRLER 271 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: 352 Number of extensions: 12 Number of successful extensions: 2 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: 281 Length adjustment: 29 Effective length of query: 405 Effective length of database: 252 Effective search space: 102060 Effective search space used: 102060 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: 49 (23.5 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