Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized)
to candidate Ac3H11_3326 Amino acid ABC transporter, permease protein
Query= reanno::pseudo3_N2E3:AO353_16285 (248 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3326 Length = 260 Score = 106 bits (265), Expect = 4e-28 Identities = 66/218 (30%), Positives = 111/218 (50%), Gaps = 13/218 (5%) Query: 25 FITGLGWTIAIAIVAWIIALMLGSVLGVMRTVPNRLVSGIATCYVELFRNVPLLVQLFIW 84 F G T+ + +++ + L+LG+ + RT +V A+ Y+ + R PLLVQ+ Sbjct: 52 FSDGARTTLWLTLISGSVGLVLGTGAALARTARWAVVRWAASFYIWVIRGTPLLVQILFV 111 Query: 85 YFLVPDLLPQ-NLQDWYKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGIQALPRGQES 143 YF +P L+P NL D + + V+ LGL A E +R G+ A+PRGQ Sbjct: 112 YFALPVLVPGLNLPD------------FAAAVLALGLNVGAYNAEAIRAGLLAVPRGQTE 159 Query: 144 AARAMGFKLPQIYWNVLLPQAYRIVIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAE 203 AA+A+G ++++V+ PQA++I +PPL S F+ + K+SS+A IG++EL + Sbjct: 160 AAKALGLGRMHVFFDVVFPQAFKISLPPLVSNFVALLKDSSLAYAIGVVELTNVGNRIQS 219 Query: 204 FSANLFEAFTLATLIYFTLNMSLMLLMRMVEKKVAVPG 241 + + + Y L + + VE + V G Sbjct: 220 ATFQPIATLSTVAITYLLLTTLVTQISNAVEYRFDVEG 257 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: 161 Number of extensions: 10 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: 260 Length adjustment: 24 Effective length of query: 224 Effective length of database: 236 Effective search space: 52864 Effective search space used: 52864 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