Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate HSERO_RS19345 HSERO_RS19345 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >FitnessBrowser__HerbieS:HSERO_RS19345 Length = 244 Score = 248 bits (634), Expect = 7e-71 Identities = 128/250 (51%), Positives = 176/250 (70%), Gaps = 11/250 (4%) Query: 14 ALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIL 73 A+++I+DLHK +G +VL GV L +Q+G +V +IG SGSGK+TLLRC+N LE+ G I Sbjct: 3 AIVKIKDLHKSFGSNKVLNGVSLDVQKGQMVAIIGKSGSGKSTLLRCLNGLEKVDAGDI- 61 Query: 74 LDGESIGYHEVNGKRVRHSEKV-IAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKL 132 +V G + H +K+ + + R G+ FQ +NLFPHLT +N+TL L +KK+ Sbjct: 62 ---------QVCGHDIHHPDKLNLRELRKQVGIVFQSYNLFPHLTVERNITLALTTIKKM 112 Query: 133 HKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALD 192 ++A +A K L+ VGL ++D YP QLSGGQ QRVAIAR++AM P LMLFDEVTSALD Sbjct: 113 STEQAKTIAHKVLQLVGLENKKDAYPEQLSGGQAQRVAIARSLAMAPELMLFDEVTSALD 172 Query: 193 PELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQ 252 PEL EVL V++ LA GMTM+LVTHEM FA +++D +VFM+QG++ E GPP ELF P+ Sbjct: 173 PELTAEVLKVMEDLARGGMTMVLVTHEMAFARKLADVLVFMHQGQVWEIGPPDELFSHPK 232 Query: 253 SPRLAEFLKN 262 + L +F+ + Sbjct: 233 TAELQKFVSS 242 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: 178 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: 244 Length adjustment: 24 Effective length of query: 241 Effective length of database: 220 Effective search space: 53020 Effective search space used: 53020 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