Align ABC transporter for D-glucosamine, permease component 1 (characterized)
to candidate AO353_10020 AO353_10020 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_21715 (220 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10020 Length = 278 Score = 135 bits (341), Expect = 6e-37 Identities = 78/199 (39%), Positives = 115/199 (57%), Gaps = 4/199 (2%) Query: 18 LAGLGLGLELALVSIAIGCVIGLLMAFALLSKHRALRVLASVYVTVIRNTPILVLILLIY 77 L G L L L L SI ++G + A A LSK +AS Y + R TP+L+ ILLIY Sbjct: 72 LQGAALTLFLCLCSIVASSLLGFITALARLSKSAVAFGIASFYASFFRGTPLLIQILLIY 131 Query: 78 FALPSLGIRLDKLPSFIITLSLYAGAYLTEVFRGGLLSIPKGLREAGLAIGLGEWQVKAY 137 LP LGI + + II LSL GAYL+E+FR G++ +P G REA LA+G+ E + Sbjct: 132 LGLPQLGIVPGAIAAGIIALSLNYGAYLSEIFRAGIVGVPHGQREASLALGMRESVIFWR 191 Query: 138 VTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVESYRVIETWLVTTAL 197 VT+P +R ++P +N FIS+ KD+SL + + V E+ + A+ SYR IE + Sbjct: 192 VTLPQAMRTIIPPTTNQFISMLKDSSLISVMGVWEVMFLAQSYGRSSYRYIEMLSTAAII 251 Query: 198 YVAACYLIAMLLRYLEQRL 216 Y +L+++ L ++ R+ Sbjct: 252 Y----WLLSIGLELIQARM 266 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: 155 Number of extensions: 8 Number of successful extensions: 1 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: 278 Length adjustment: 24 Effective length of query: 196 Effective length of database: 254 Effective search space: 49784 Effective search space used: 49784 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: 46 (22.3 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