Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate SM_b20706 SM_b20706 amino acid uptake ABC transporter substrate-binding protein precursor
Query= reanno::pseudo3_N2E3:AO353_03055 (258 letters) >FitnessBrowser__Smeli:SM_b20706 Length = 258 Score = 201 bits (512), Expect = 1e-56 Identities = 123/258 (47%), Positives = 153/258 (59%), Gaps = 5/258 (1%) Query: 1 MKKLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEE 60 M+KL+L ALA + LS A EK LKIG E AYPPF G I GFD +IG ALCE Sbjct: 1 MRKLILALALAGTALSSSAVAAEK-LKIGTEGAYPPFNFVDSSGKIGGFDVEIGLALCER 59 Query: 61 MKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAGT 120 MKV+C V Q++DG+IP L +K D I++SM IT++RKK V FTN YY G Sbjct: 60 MKVECEVVAQDWDGIIPGLLAKKYDMIIASMFITEERKKQVAFTNPYYLAAMTHAAPKGA 119 Query: 121 QVSDNLAE-LKGKKIGVQRGSIHNRFAEEVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTV 179 +S E L+GK IG Q G+ + V AEIK Y +Q+E LD+ GRLD V Sbjct: 120 GISAFSNEALQGKVIGAQSGTTQADYIAAVYP--DAEIKLYPTQDEANLDMVNGRLDLQV 177 Query: 180 ADATLLDDGFLKTDSGKGFA-FVGPAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAIR 238 D L D K D GKG VG TD+K+ GDG+GIAVR+ D +K+N A+ IR Sbjct: 178 GDMLPLLDWVTKNDDGKGCCELVGEPITDKKFVGDGVGIAVRQEDNEMREKLNKALDEIR 237 Query: 239 ANGKYKQIQDKYFNFDIY 256 A+G YK+I DKYF D+Y Sbjct: 238 ADGTYKKINDKYFTIDVY 255 Lambda K H 0.318 0.138 0.395 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: 223 Number of extensions: 16 Number of successful extensions: 3 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: 258 Length of database: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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