Align ABC transporter for D-glucosamine, permease component 1 (characterized)
to candidate Pf6N2E2_4281 Amino acid ABC transporter, permease protein
Query= reanno::pseudo3_N2E3:AO353_21715 (220 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4281 Length = 265 Score = 137 bits (344), Expect = 3e-37 Identities = 80/199 (40%), Positives = 118/199 (59%), Gaps = 4/199 (2%) Query: 18 LAGLGLGLELALVSIAIGCVIGLLMAFALLSKHRALRVLASVYVTVIRNTPILVLILLIY 77 L G L L L L SI ++G + A A LS +AS Y + R TP+L+ ILLIY Sbjct: 59 LQGAVLTLFLCLCSIVASSLLGFITALARLSSSAVAFGIASFYASFFRGTPLLIQILLIY 118 Query: 78 FALPSLGIRLDKLPSFIITLSLYAGAYLTEVFRGGLLSIPKGLREAGLAIGLGEWQVKAY 137 LP LG+ + + II LSL GAYL+E+FR G+L +P G REA LA+GL E + Sbjct: 119 LGLPQLGVVPGAIAAGIIALSLNYGAYLSEIFRAGILGVPHGQREASLALGLSETVIFWR 178 Query: 138 VTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVESYRVIETWLVTTAL 197 VT+P +R ++P +N FIS+ KD+SL + + V E+ + A+ SYR IE ++TTA Sbjct: 179 VTLPQAMRTIIPPTTNQFISMLKDSSLISVMGVWEVMFLAQSYGRSSYRYIE--MLTTAA 236 Query: 198 YVAACYLIAMLLRYLEQRL 216 + +L+++ L ++ R+ Sbjct: 237 II--YWLMSIALELIQARM 253 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: 265 Length adjustment: 23 Effective length of query: 197 Effective length of database: 242 Effective search space: 47674 Effective search space used: 47674 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