Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_017221498.1 A923_RS0109795 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >NCBI__GCF_000276805.1:WP_017221498.1 Length = 251 Score = 225 bits (573), Expect = 8e-64 Identities = 126/244 (51%), Positives = 157/244 (64%), Gaps = 11/244 (4%) Query: 20 DLHKQY-GPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLDGES 78 D+ K Y LK V +T++RG VV +IG SGSGK+T LR +N LE G I +DG + Sbjct: 16 DVDKIYPNKCHALKKVSVTVKRGEVVVIIGPSGSGKSTFLRTLNQLETVTEGDITIDGIN 75 Query: 79 IGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHKDEAV 138 + N +R + GM FQ FNLFPHL+ +NV L LKV L K++ Sbjct: 76 MYDSSTNINTLREN----------VGMVFQSFNLFPHLSVKENVKLAPLKVSNLGKEQVE 125 Query: 139 VLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPELVGE 198 A L RVGL E+ D YP QLSGGQQQRVAIARA+AM P LMLFDE TSALDPE+VGE Sbjct: 126 KDAISLLTRVGLAEKVDVYPSQLSGGQQQRVAIARALAMKPDLMLFDEPTSALDPEMVGE 185 Query: 199 VLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSPRLAE 258 VL V+K LAE+GMTM++VTHEM FA EV+D+++FM G++ P FE P PRL + Sbjct: 186 VLEVMKSLAEEGMTMVVVTHEMGFANEVADRVLFMEDGQLLVDDVPANFFENPSHPRLKK 245 Query: 259 FLKN 262 FL + Sbjct: 246 FLSS 249 Lambda K H 0.319 0.135 0.379 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: 174 Number of extensions: 7 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: 265 Length of database: 251 Length adjustment: 24 Effective length of query: 241 Effective length of database: 227 Effective search space: 54707 Effective search space used: 54707 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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