Align GtsB (GLcF), component of Glucose porter, GtsABCD (characterized)
to candidate BPHYT_RS22775 BPHYT_RS22775 sugar ABC transporter permease
Query= TCDB::Q88P37 (302 letters) >FitnessBrowser__BFirm:BPHYT_RS22775 Length = 325 Score = 141 bits (356), Expect = 2e-38 Identities = 90/290 (31%), Positives = 153/290 (52%), Gaps = 6/290 (2%) Query: 11 SPLDALQRWLPKLVLAPSMFIVLVGFYGYILWTFVLSFTTSTFLPTYKWAGLAQYARLFD 70 SP QR L LAP+ +V + IL T LSF + + GLA Y LF Sbjct: 42 SPTARRQRRAAFLFLAPACVMVAIYVVWPILSTIRLSFFNWDGMSEPSFVGLANYVELFH 101 Query: 71 NDRWWVASKNLLLFGGLFIAISLAIGVLLAVLLDQRIRREGFIRTIYLYPMALSMIVTGT 130 ++ A KN L++ LF+ ++ +G+ +A+ L+Q + +++++ P LS +V G Sbjct: 102 AQTFYTALKNNLIWLLLFL-LAPPMGLAVALYLNQAVAGIRIVKSLFFAPFVLSGVVVGL 160 Query: 131 AWKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLR 190 + W +P GL ++ G + L DP + +V AA+W + + M ++L GL Sbjct: 161 IFSWFYDPTFGLLAVILGHG-----VPVLGDPRYATFGIVFAALWPQTAYCMILYLTGLT 215 Query: 191 GVDPSIIRAAQMDGASLPRIYWTVVLPSLRPVFFSALMILSHIAIKSFDLVAAMTAGGPG 250 ++ I AA+M+GA + W V+LP LRP F A+++ A++SFDL++ MT GGP Sbjct: 216 SLNAEQIEAARMEGARGWSMLWHVILPQLRPTTFMAIVVTIIGALRSFDLISVMTGGGPF 275 Query: 251 YSSDLPAMFMYSFTFSRGQMGMGSASAILMLGAILAILVPYLYSELRSKR 300 SS + A +MY ++G +A A+++ +L +V +L LR+++ Sbjct: 276 ESSTVLAYYMYDQAIKYYRIGYSAAVAVVLFAIMLVYIVYHLRRMLRAEQ 325 Lambda K H 0.330 0.142 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: 251 Number of extensions: 14 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: 302 Length of database: 325 Length adjustment: 27 Effective length of query: 275 Effective length of database: 298 Effective search space: 81950 Effective search space used: 81950 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 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