Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate WP_085634732.1 MGEO_RS00455 sugar ABC transporter permease
Query= reanno::WCS417:GFF4323 (302 letters) >NCBI__GCF_002115805.1:WP_085634732.1 Length = 305 Score = 351 bits (901), Expect = e-101 Identities = 165/293 (56%), Positives = 222/293 (75%), Gaps = 8/293 (2%) Query: 16 LQRWLPKLVLAPSMFIVLVGFYGYILWTFVLSFTNSTFLP--------TYKWAGLAQYAR 67 LQ WLPKLVL+PS+ +VL+ YG+IL+T +SFT+S LP T + G + Y + Sbjct: 13 LQNWLPKLVLSPSLAMVLIFVYGFILFTVYVSFTDSRILPFVNNDGQRTLELIGFSNYEK 72 Query: 68 LFDNDRWWVASKNLAVFGGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIV 127 LF W ++ N+A F G++IGI +G+ LAIFLDQKIR EG +RTIYLYPMALS IV Sbjct: 73 LFSLSHWEISLWNMATFAGLYIGICTCLGLGLAIFLDQKIRAEGALRTIYLYPMALSFIV 132 Query: 128 TGTAWKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLA 187 TGTAWKW L+PG+GL+ +++ WGW F DW+ + D +Y +V+AAVWQ SGF+MAMFLA Sbjct: 133 TGTAWKWFLDPGIGLENVMQSWGWTSFEFDWIKNRDYAIYTVVLAAVWQTSGFVMAMFLA 192 Query: 188 GLRGVDQSIVRAAQIDGASMPRIYWSVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMTAG 247 GLRG+D I++AAQ+DGAS +Y +++P LRP F SA +IL+H+AIK+FDLV A+T G Sbjct: 193 GLRGIDNEILKAAQMDGASNWNLYRRIIIPQLRPAFLSAFVILSHLAIKTFDLVIALTGG 252 Query: 248 GPGYSSDLPAMFMYSFTFSRGQMGMGSASAILMLGAILAIIVPYLYSELRTKR 300 GPG +++LPA FMYS+TFSR QMG+G++SA++ML I AI++PYLY+ELR K+ Sbjct: 253 GPGRATELPATFMYSYTFSRNQMGIGASSAVIMLMTIAAIMIPYLYAELREKK 305 Lambda K H 0.330 0.141 0.455 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: 385 Number of extensions: 14 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: 302 Length of database: 305 Length adjustment: 27 Effective length of query: 275 Effective length of database: 278 Effective search space: 76450 Effective search space used: 76450 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 (21.8 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