Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate GFF2207 HP15_2161 sugar ABC transporter, permease protein
Query= reanno::Smeli:SMc03063 (380 letters) >FitnessBrowser__Marino:GFF2207 Length = 269 Score = 127 bits (319), Expect = 4e-34 Identities = 73/232 (31%), Positives = 124/232 (53%), Gaps = 7/232 (3%) Query: 146 PPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLA 205 P FTLDNYA + + ++NS+ + VI +L+A AAYA + F G L Sbjct: 45 PQNFTLDNYAVIFTDPSWYNGYINSMIYVSINVVITLLVALPAAYAFSRYKFLGDKHLFF 104 Query: 206 VVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAG 265 ++ + P + L+P QLY+ +G F T++ + LAH F +PLA+++L +M+G Sbjct: 105 WLLSNRMAPPAVFLLPFFQLYSSIGLF-----DTHIAVALAHCLFNVPLAVWILEGFMSG 159 Query: 266 LPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDK 325 +PRE E A +DG S FVK+ LP+ + A F F+++W +LL+A D Sbjct: 160 VPREYDEMAYIDGYSFPKFFVKVFLPMIRSGIGVTAFFAFMFSWVELLLARTLTSV--DA 217 Query: 326 LVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSV 377 + + +G+ G +W +L A+ +TI+ L+V + ++ ++ +G G V Sbjct: 218 QPIGAIMTRTIGASGIDWGVLAAAGSLTIIPGLLVIWFVRNHVAKGFALGRV 269 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: 234 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: 269 Length adjustment: 28 Effective length of query: 352 Effective length of database: 241 Effective search space: 84832 Effective search space used: 84832 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