Align TreT, component of Trehalose porter (characterized)
to candidate WP_049988752.1 LT39_RS01710 sugar ABC transporter permease
Query= TCDB::Q97ZC2 (275 letters) >NCBI__GCF_000784335.1:WP_049988752.1 Length = 312 Score = 112 bits (279), Expect = 1e-29 Identities = 82/269 (30%), Positives = 140/269 (52%), Gaps = 15/269 (5%) Query: 10 LLVLPALAYV--ISFAFFPTIEAVYLSFQDPHGGFSLYNYKELSYFNLSSAIINTIVVTI 67 +LVL L+ V I+ + +E +L +P L NY+ + ++++ T+ + Sbjct: 37 VLVLGILSIVPLIALLWLSAMEVNFLPGHEPTF-VGLENYQAMFNSTVANSWKVTVFYIV 95 Query: 68 GALAIQLALGFLVASVLSREFFGKRALSTITIIPMGIATVVAAVTFSFVFQTSGGYANTI 127 GAL++Q+ LG +A +L R G+ L+ I I+PM IA VV + + F+ S G + Sbjct: 96 GALSLQITLGTAIALLLDRVSRGENVLTGIIIMPMMIAPVVVGLLWQFLLDPSFGLYTWL 155 Query: 128 LHSLFGLNVNW--YQSSISSLLVVMIADSWKNTPIVALILLAGMSSIPKELYYASAIDGA 185 L+ + GL S S+L+ V++ D+W+ TP+V LI+LAG+ ++P++LY A+ +DGA Sbjct: 156 LNQI-GLFTESPILGSQPSALIAVIVMDTWQWTPLVVLIVLAGLKAVPRQLYEAARVDGA 214 Query: 186 GPIRRFFYITLPNLRSFIGISLILRGVQEFNIFALPLILIGEHPPLLTTLI-YDLYTTTF 244 F Y+TLP L+ + I+L+LR + F I G P T +I + +Y + Sbjct: 215 TFWTEFRYVTLPMLKPALAIALLLRSMDLIRYFTKIFITTGGGPASSTKIIGFLVYEESL 274 Query: 245 --------PEVGLALASATILLGFILVFS 265 +G+ + T+LLG S Sbjct: 275 RFYNLGYGAAMGIGMLIVTVLLGIFFTES 303 Lambda K H 0.328 0.143 0.414 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: 209 Number of extensions: 8 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: 275 Length of database: 312 Length adjustment: 26 Effective length of query: 249 Effective length of database: 286 Effective search space: 71214 Effective search space used: 71214 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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