Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate N515DRAFT_3133 N515DRAFT_3133 carbohydrate ABC transporter membrane protein 2, CUT1 family (TC 3.A.1.1.-)
Query= reanno::Smeli:SMc03063 (380 letters) >FitnessBrowser__Dyella79:N515DRAFT_3133 Length = 273 Score = 152 bits (385), Expect = 8e-42 Identities = 90/234 (38%), Positives = 137/234 (58%), Gaps = 8/234 (3%) Query: 146 PPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLA 205 P TL NY E+ AG+GR LNSL V+ T++ + A YA A + F GR L Sbjct: 48 PTHATLANYHELFERAGMGRYLLNSLGVSSAITLLSLAFNLMAGYAFAKLRFSGRERLFQ 107 Query: 206 VVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAG 265 V++G LV+P Q++++PL L +G V++ + + T FG I+L+R Y G Sbjct: 108 VLLGGLVIPAQVAMLPLFLLLKYLGL---VNSYAAVVVPAMATIFG----IFLVRQYARG 160 Query: 266 LPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDK 325 +P ++ME+AR+DGA + IFV+I+LPL P + + AIF FL WND + ++ L G + Sbjct: 161 IPDDLMEAARIDGAGELRIFVQIVLPLLKPIMVTLAIFTFLTAWNDFMWPLIAL-TGQEH 219 Query: 326 LVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379 L L +L + E++ A + +T++ L++F ALQRY ++GLL GSVKG Sbjct: 220 YTLPIALASLSREHVQDSELMMAGSVVTVLPVLVLFLALQRYYLQGLLLGSVKG 273 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: 253 Number of extensions: 9 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: 273 Length adjustment: 28 Effective length of query: 352 Effective length of database: 245 Effective search space: 86240 Effective search space used: 86240 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