Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate AZOBR_RS18060 AZOBR_RS18060 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_2050 (263 letters) >FitnessBrowser__azobra:AZOBR_RS18060 Length = 244 Score = 264 bits (674), Expect = 2e-75 Identities = 138/246 (56%), Positives = 178/246 (72%), Gaps = 10/246 (4%) Query: 13 LLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIML 72 L+ I ++K++G +EVLKG++L ++RG VV +IG SGSGK+TLLRCVN LE G IM+ Sbjct: 3 LIAITEVKKRFGDVEVLKGINLDVERGEVVAIIGKSGSGKSTLLRCVNGLEMIDDGSIMV 62 Query: 73 DGESIGYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLPK 132 G + DD+ K +R GM FQQFNLFPHL+A +NV L + VKK P Sbjct: 63 AGAQLINDDLHLKALR----------LKVGMIFQQFNLFPHLSAGRNVMLSQMVVKKTPA 112 Query: 133 DEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPE 192 EA A+A + LERVGL + D +P QLSGGQQQRVAIARA++M P +L DE+TSALDPE Sbjct: 113 REAEAMARRMLERVGLGHKFDAYPDQLSGGQQQRVAIARALSMQPMALLCDEITSALDPE 172 Query: 193 LVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSP 252 LV EVL V+K LA DGMT+++VTHEMRFA EV D++VFM+QGR+ E GPP+E+F P++P Sbjct: 173 LVNEVLAVVKELAADGMTLMMVTHEMRFAREVCDRVVFMHQGRVHEIGPPEEVFGNPRTP 232 Query: 253 RLAEFL 258 L +FL Sbjct: 233 ELRQFL 238 Lambda K H 0.320 0.138 0.392 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: 184 Number of extensions: 4 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: 263 Length of database: 244 Length adjustment: 24 Effective length of query: 239 Effective length of database: 220 Effective search space: 52580 Effective search space used: 52580 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: 46 (22.3 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