Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate PfGW456L13_1967 Arginine/ornithine ABC transporter, ATP-binding protein AotP
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1967 Length = 254 Score = 249 bits (635), Expect = 5e-71 Identities = 128/249 (51%), Positives = 178/249 (71%), Gaps = 1/249 (0%) Query: 16 LEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLD 75 LE++DLHK+YG EVLKGV L G+V+++IGSSGSGK+T LRC+N+LE+ G+ILL+ Sbjct: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGRILLN 63 Query: 76 GESIGY-HEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHK 134 E + +G K + + R+ M FQ FNL+ H+TAL+N+ + V + K Sbjct: 64 NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTALENIMEAPVHVLGVSK 123 Query: 135 DEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPE 194 EA AE +L +VG+ R+D YPG +SGG+QQRVAIARA+AM P +MLFDE TSALDPE Sbjct: 124 AEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183 Query: 195 LVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSP 254 LVG+VL V++ LA++G TM++VTHEM FA EVS+++VF+++G +EE G P+E+ PQS Sbjct: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243 Query: 255 RLAEFLKNT 263 RL +FL + Sbjct: 244 RLQQFLSGS 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: 195 Number of extensions: 11 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: 254 Length adjustment: 24 Effective length of query: 241 Effective length of database: 230 Effective search space: 55430 Effective search space used: 55430 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