Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate SMc00139 SMc00139 amino acid ABC transporter permease
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__Smeli:SMc00139 Length = 267 Score = 94.0 bits (232), Expect = 5e-24 Identities = 78/261 (29%), Positives = 125/261 (47%), Gaps = 19/261 (7%) Query: 184 VSAGIGLVVAALFWLYAAAPIEAALQSALPLALPEVD-SDQFG-GFLLALVIGVTAIVVS 241 +SAG+ + A + L A I S LA + D+ GFL+ + V + V Sbjct: 8 LSAGLAWIGAIIDPLCGPAGIFRWFGSGTLLACGDAGWGDEIAYGFLVTASLAVATLPVG 67 Query: 242 LPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTA----SLLLQYFLPP----- 292 L +G +AL +QS+ ++ RG+P + LF +L+Q FL Sbjct: 68 LVIGFFVALAKQSEEKSLRLAGNIYTTIFRGLPELLTLFIVYYGLQILVQQFLATVGYEG 127 Query: 293 GTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQA 352 + + +I + + +AY +EV+ A+P GQYEA DALGL + RLII+PQ Sbjct: 128 AVEINAFVAGMIALGVVFSAYCSEVLLSAFKAIPHGQYEAGDALGLHRGKTMRLIILPQL 187 Query: 353 LKISIPGIVSSFIGLFKDTTLVAFVGLFDPLK--GISNVVRSDMAWKGTYWEPYIFVALI 410 ++I++PG+ + ++ L KDT LV+ +GL D L+ GI+ V +E + ++ Sbjct: 188 IRIALPGLGNLWMALLKDTALVSVIGLPDILRQTGIAARVTKHA------FEFFGIACVL 241 Query: 411 FFLFNFSMSRYSMYLERKLKR 431 F + S LER KR Sbjct: 242 FLVLAMISSVVFSALERSTKR 262 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: 319 Number of extensions: 20 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: 267 Length adjustment: 28 Effective length of query: 406 Effective length of database: 239 Effective search space: 97034 Effective search space used: 97034 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