Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate GFF3087 HP15_3030 histidine/lysine/arginine/ornithine transporter subunit
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >FitnessBrowser__Marino:GFF3087 Length = 256 Score = 261 bits (668), Expect = 8e-75 Identities = 132/251 (52%), Positives = 183/251 (72%), Gaps = 1/251 (0%) Query: 11 ASQALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGG 70 A Q+ L RD++K + LEVLKG+ L ++G+VV+LIGSSGSGK+T LRC+N+LE G Sbjct: 2 ADQSPLICRDIYKTFDQLEVLKGISLETRKGDVVSLIGSSGSGKSTFLRCINLLETPTSG 61 Query: 71 QILLDGESIGYH-EVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKV 129 I++ G+ I + G+R+ K + RA M FQ FNL+ H+T L+N+ + V Sbjct: 62 DIIVHGDPIRFTTNRKGERIPADNKQVELIRAKLSMVFQSFNLWSHMTVLENIIEAPVHV 121 Query: 130 KKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTS 189 K+ K EA+ AE +L +VG+ ER+D+YP Q+SGGQQQR AIARA+AM P +MLFDE TS Sbjct: 122 LKVPKKEAIERAEAYLNKVGIYERKDYYPAQMSGGQQQRAAIARALAMEPEVMLFDEPTS 181 Query: 190 ALDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFE 249 ALDPELVGEVL V++GLAE+G TM++VTHEM FA +VS +++F++QG IEEQG P+++F+ Sbjct: 182 ALDPELVGEVLKVMQGLAEEGRTMIVVTHEMAFARDVSSQVLFLHQGVIEEQGTPEKVFD 241 Query: 250 RPQSPRLAEFL 260 P S R+ +FL Sbjct: 242 HPDSERMKQFL 252 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: 185 Number of extensions: 8 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: 256 Length adjustment: 24 Effective length of query: 241 Effective length of database: 232 Effective search space: 55912 Effective search space used: 55912 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 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