Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate GFF3170 PS417_16225 sugar ABC transporter permease
Query= reanno::Smeli:SMc03063 (380 letters) >FitnessBrowser__WCS417:GFF3170 Length = 266 Score = 117 bits (294), Expect = 3e-31 Identities = 71/232 (30%), Positives = 122/232 (52%), Gaps = 7/232 (3%) Query: 146 PPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLA 205 P FTL NY + + +LNSL +TVI + +A AAYA + F G L Sbjct: 42 PQDFTLANYKVIFTDPSWYTGYLNSLYYVSLNTVISLSVALPAAYAFSRYRFLGDKHLFF 101 Query: 206 VVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAG 265 ++ + P + L+P QLY+ +G F T++ + LAH F +PLA+++L +M+G Sbjct: 102 WLLTNRMAPPAVFLLPFFQLYSSIGLF-----DTHIAVALAHCLFNVPLAVWILEGFMSG 156 Query: 266 LPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDK 325 +P+EI E+A +DG S FVKI +PL + A F F+++W +LL+A Sbjct: 157 VPKEIDETAYIDGYSFPKFFVKIFIPLIGSGIGVTAFFCFMFSWVELLLARTLTSVNAKP 216 Query: 326 LVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSV 377 + + + + G +W +L A+ +TI+ ++V + ++ ++ +G G V Sbjct: 217 IAAV--MTRTVSASGIDWGVLAAAGVLTILPGMLVIWFVRNHVAKGFALGRV 266 Lambda K H 0.324 0.139 0.418 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: 247 Number of extensions: 15 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: 380 Length of database: 266 Length adjustment: 27 Effective length of query: 353 Effective length of database: 239 Effective search space: 84367 Effective search space used: 84367 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 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