Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 2 (characterized)
to candidate WP_052597074.1 VV02_RS15280 sugar ABC transporter permease
Query= reanno::WCS417:GFF2492 (297 letters) >NCBI__GCF_001190945.1:WP_052597074.1 Length = 302 Score = 125 bits (315), Expect = 9e-34 Identities = 90/290 (31%), Positives = 146/290 (50%), Gaps = 10/290 (3%) Query: 4 TTPKNRLANPGWFLVSPSVALLLLWMIVPLGMTLYFSLIRYNLLYPGENEFVGLENFTYF 63 +T + R A G V P+V + ++ +P+ SL Y L G+ FVG +N++ Sbjct: 13 STERRREAITGILFVLPTVVIFGIFKFLPILGAGAMSLTDYQL--NGDYTFVGADNYSRI 70 Query: 64 ITDSGFLPGATNTLLLVGSVLLISVVFGVLISALLEASEFLGRGLVRVLLISPFFIMPTV 123 + D F T L V + + VV + + LL + GL R LL P+ + Sbjct: 71 LQDDAFWQSLKVTGLYVVIFVPLIVVVSLAGAVLLHQMQRY-TGLFRSLLFVPYLCSFVL 129 Query: 124 GALIWKNLIFHPVSGILAAVWKFFGAEPVDWLAHYPLL---SIIIIVSWQWLPFAILLLM 180 ++W + G L A G V +++ LL S+ ++ W+ +++L+ + Sbjct: 130 AGIVWTWIF--ATDGPLNAALGGLGFGSVPFISGSQLLVLGSLAMVSVWKGFGYSMLIFL 187 Query: 181 TAMQSLDQEQKEAARLDGAGAIAIFWHLTLPHLARPIAV-VVMIETIFLLSVFAEIFTTT 239 +++L E EAAR+DGAGA FWH+TLP L RPI + V++IETI VF I+ T Sbjct: 188 AGLKALPAEVHEAARIDGAGAWRTFWHITLP-LLRPITLFVLIIETIVGFQVFDTIYVMT 246 Query: 240 NGGPGYASTNLAYLIYNQALVQFDVGMASAGGLIAVVIANIAAIILVRMI 289 GGP AS +L Y +Y++ FD G A+A G++ VI + +++ R + Sbjct: 247 GGGPNRASHSLIYFLYDEGFKFFDFGYAAAAGVVLFVIVLLLSLVQQRTV 296 Lambda K H 0.328 0.143 0.437 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: 241 Number of extensions: 16 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: 297 Length of database: 302 Length adjustment: 27 Effective length of query: 270 Effective length of database: 275 Effective search space: 74250 Effective search space used: 74250 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