Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized)
to candidate GFF355 PS417_01810 ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_16285 (248 letters) >FitnessBrowser__WCS417:GFF355 Length = 319 Score = 129 bits (324), Expect = 7e-35 Identities = 74/224 (33%), Positives = 123/224 (54%), Gaps = 14/224 (6%) Query: 15 GVGSETYLDWFITGLGWTIAIAIVAWIIALMLGSVLGVMRTVPNRLVSGIATCYVELFRN 74 GV L + GL T+ +++V+ I+ L++G G+ R N + ++T YVEL R Sbjct: 107 GVTRHWALGPLMWGLWTTLWLSVVSGILGLIIGLATGLCRLSSNPTLRDLSTIYVELVRG 166 Query: 75 VPLLVQLFIWYFLVPDLLPQNLQDWYKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGI 134 PLLVQ+FI+YF + +L S + + L LFT A V E VR G+ Sbjct: 167 TPLLVQIFIFYFFIGTVL--------------NLSREFAGIAALSLFTGAYVAEIVRAGV 212 Query: 135 QALPRGQESAARAMGFKLPQIYWNVLLPQAYRIVIPPLTSEFLNVFKNSSVASLIGLMEL 194 Q++ RGQ AAR++G Q +V+LPQA++ V+PPL +F+++ K++S+ S+I + EL Sbjct: 213 QSITRGQNEAARSLGLSASQSMRHVVLPQAFKRVLPPLAGQFISLVKDTSLVSVIAITEL 272 Query: 195 LAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRMVEKKVA 238 L ++ S + FE +Y +N+ L + +E+++A Sbjct: 273 LKSGREVITTSFSPFEILFCVAGLYLLINLPLSKMASRLERRLA 316 Lambda K H 0.326 0.139 0.432 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: 191 Number of extensions: 6 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: 248 Length of database: 319 Length adjustment: 26 Effective length of query: 222 Effective length of database: 293 Effective search space: 65046 Effective search space used: 65046 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 (21.7 bits) S2: 47 (22.7 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