Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit
Query= reanno::pseudo5_N2C3_1:AO356_00470 (220 letters) >NCBI__GCF_000016765.1:WP_012048835.1 Length = 374 Score = 82.4 bits (202), Expect = 1e-20 Identities = 70/202 (34%), Positives = 91/202 (45%), Gaps = 23/202 (11%) Query: 17 TLWAGFLTSVQ-CSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLIRGTPVFVLVL 75 T W G L C+L IV G+ + +V L L F F L TP FV VL Sbjct: 190 TAWRGHLHKASLCTLGTIVAGSALWIVLDLGLARDVPHFDR-FNFTGGLTL-TPEFVAVL 247 Query: 76 ACFYMAPALGWQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASQAIGLTFYQS 135 W G ++ + AEIVRG L +PRGQ EAS+A+GL+ QS Sbjct: 248 ----------W----------GSVIYASAFAAEIVRGGLDGVPRGQWEASRALGLSKRQS 287 Query: 136 LGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLFA 195 L V++PQALR I+P + I+K STL V+G +L I T LE Sbjct: 288 LRLVIVPQALRMIVPPMNSQFITILKNSTLALVVGYPDLNFVANTAINHTGQGLEGVAIL 347 Query: 196 GFLFFIINYAIELLGRHIEKRV 217 +FF + AI L + RV Sbjct: 348 MLVFFTLASAISLAMNRLNARV 369 Score = 32.7 bits (73), Expect = 9e-06 Identities = 23/64 (35%), Positives = 32/64 (50%), Gaps = 4/64 (6%) Query: 16 DTL-WA---GFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLIRGTPVF 71 DT+ WA G S+ +LL IVL T+ G+ L G R +VDL+R P+ Sbjct: 69 DTIAWAFVVGLGNSIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRNVPLV 128 Query: 72 VLVL 75 V +L Sbjct: 129 VQLL 132 Lambda K H 0.330 0.142 0.443 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: 222 Number of extensions: 11 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 220 Length of database: 374 Length adjustment: 26 Effective length of query: 194 Effective length of database: 348 Effective search space: 67512 Effective search space used: 67512 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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