Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate GFF3538 PS417_18120 arginine ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >FitnessBrowser__WCS417:GFF3538 Length = 259 Score = 278 bits (712), Expect = 6e-80 Identities = 137/251 (54%), Positives = 186/251 (74%), Gaps = 1/251 (0%) Query: 11 ASQALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGG 70 + + ++E D+HK +G L++LKG+ L ++RG VV LIG+SGSGKTT +RC+N+LE+ QGG Sbjct: 5 SEELIIEALDIHKSFGALQILKGISLQVRRGEVVVLIGASGSGKTTFIRCINLLEDIQGG 64 Query: 71 QILLDGESIGYHE-VNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKV 129 +I ++G ++GY E +G VR SE+ IA+ R GM FQ+FNLFPH+TAL+N+ ++V Sbjct: 65 RIRVNGRAMGYRERSDGSLVRDSERNIARQRRDIGMVFQRFNLFPHMTALENIIEAPIQV 124 Query: 130 KKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTS 189 + +A+ A L RVGL ++ HYP LSGGQQQRVAIARA+AM P MLFDE TS Sbjct: 125 LGTPRAQALEQARGLLARVGLADKASHYPAMLSGGQQQRVAIARALAMKPQAMLFDEPTS 184 Query: 190 ALDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFE 249 ALDPE VGEVL V+K LAE+GMTM++VTHEM FA EV+D++V ++QG + EQGPP+++F Sbjct: 185 ALDPETVGEVLQVMKELAEEGMTMVVVTHEMGFAREVADRVVVLDQGELIEQGPPEQIFS 244 Query: 250 RPQSPRLAEFL 260 P PR FL Sbjct: 245 HPSHPRTRAFL 255 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: 190 Number of extensions: 9 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: 259 Length adjustment: 25 Effective length of query: 240 Effective length of database: 234 Effective search space: 56160 Effective search space used: 56160 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