Align ABC transporter for D-glucosamine, permease component 1 (characterized)
to candidate H281DRAFT_02614 H281DRAFT_02614 L-glutamine ABC transporter membrane protein
Query= reanno::pseudo3_N2E3:AO353_21715 (220 letters) >FitnessBrowser__Burk376:H281DRAFT_02614 Length = 218 Score = 146 bits (369), Expect = 3e-40 Identities = 76/216 (35%), Positives = 125/216 (57%), Gaps = 1/216 (0%) Query: 4 QLNFAAVWRDFDTLLAGLGLGLELALVSIAIGCVIGLLMAFALLSKHRALRVLASVYVTV 63 Q + + + L+ G L + + + +A G +GL+ + + +A Y+ Sbjct: 2 QFDLSVIVDAVPALMHGARLTVLITIAGLAGGMFVGLVFGLMRAYGNTLCQKIAFTYIEF 61 Query: 64 IRNTPILVLILLIYFALPSL-GIRLDKLPSFIITLSLYAGAYLTEVFRGGLLSIPKGLRE 122 +R TPI+V ++ IYFALP L +R+D + + I+++ + +GAY+ E+ RG LS+P+GL+E Sbjct: 62 VRGTPIVVQVMFIYFALPLLMHVRVDAMTAAIVSIIINSGAYIAEIVRGAFLSVPRGLKE 121 Query: 123 AGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINV 182 AGLA+G+ W+V A+V PV LR + PAL N FI KDTSL I V ELT ++I Sbjct: 122 AGLALGMPGWRVLAFVVGPVALRRMTPALGNQFIVSLKDTSLFIVIGVGELTRQGQEIMA 181 Query: 183 ESYRVIETWLVTTALYVAACYLIAMLLRYLEQRLAI 218 ++R +E W +Y+ ++ LR +E+R+ I Sbjct: 182 SNFRAVEIWTAVALIYLCMIGALSFGLRTMERRMRI 217 Lambda K H 0.329 0.143 0.416 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: 139 Number of extensions: 7 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: 220 Length of database: 218 Length adjustment: 22 Effective length of query: 198 Effective length of database: 196 Effective search space: 38808 Effective search space used: 38808 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: 45 (21.9 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