Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_172599875.1 RSPH17029_RS02015 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >NCBI__GCF_000015985.1:WP_172599875.1 Length = 249 Score = 233 bits (595), Expect = 2e-66 Identities = 123/252 (48%), Positives = 171/252 (67%), Gaps = 10/252 (3%) Query: 9 QNASQALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQ 68 Q + + ++I ++K YG VL+ V++T+ +G + + G SGSGK+TL+RC+N LEE Q Sbjct: 2 QVSDEVAIQISQMNKWYGSFHVLRDVNMTVHKGERIVICGPSGSGKSTLIRCINRLEEHQ 61 Query: 69 GGQILLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLK 128 GQI++DG + +++ +KV R+ GM FQ FNLFPHLT L+N TL + Sbjct: 62 SGQIVVDGIELT------SDLKNIDKV----RSEVGMVFQHFNLFPHLTILENCTLAPIW 111 Query: 129 VKKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVT 188 V+K K EA +A +L++V + E+ YPGQLSGGQQQRVAIAR++ M P +MLFDE T Sbjct: 112 VRKTPKKEAEEVAMHYLKKVKIPEQAHKYPGQLSGGQQQRVAIARSLCMKPRIMLFDEPT 171 Query: 189 SALDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELF 248 SALDPE++ EVL + LAE+GMTML VTHEM FA V+++++FM+QG+I EQ P E F Sbjct: 172 SALDPEMIKEVLDTMIELAEEGMTMLCVTHEMGFAQAVANRVIFMDQGQIVEQNEPGEFF 231 Query: 249 ERPQSPRLAEFL 260 P+S R FL Sbjct: 232 RNPKSERTKLFL 243 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: 194 Number of extensions: 5 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: 249 Length adjustment: 24 Effective length of query: 241 Effective length of database: 225 Effective search space: 54225 Effective search space used: 54225 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 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