Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate SMc02260 SMc02260 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >FitnessBrowser__Smeli:SMc02260 Length = 284 Score = 255 bits (652), Expect = 6e-73 Identities = 140/254 (55%), Positives = 181/254 (71%), Gaps = 2/254 (0%) Query: 10 NASQALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQG 69 +A+QA+ + DLHK++GPLEVLKGV L+ ++G+V+ +IG SGSGK+TLLRC+NMLE Sbjct: 30 DAAQAIA-VTDLHKRFGPLEVLKGVSLSARQGDVIAIIGGSGSGKSTLLRCINMLELPSA 88 Query: 70 GQILLDGESIGYH-EVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLK 128 GQI + GE I + +G + K + + R GM FQ FNL+ H+T LQNV + Sbjct: 89 GQISVHGEEIRMKPDGHGGLMPADRKQVQRIRTQLGMVFQSFNLWQHMTILQNVIEAPVH 148 Query: 129 VKKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVT 188 V K EAV AE L RVGL E+RD YP LSGGQQQR AIARA+A+ P +MLFDE T Sbjct: 149 VLGKTKAEAVETAEALLRRVGLYEKRDAYPAFLSGGQQQRAAIARALAIQPLVMLFDEPT 208 Query: 189 SALDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELF 248 SALDPELVGEVLSVI LA + TM+LVTHEM+FA +V++ IVF++ G IEEQGPP+ +F Sbjct: 209 SALDPELVGEVLSVIGDLAREERTMVLVTHEMKFARDVANHIVFLHNGVIEEQGPPEAIF 268 Query: 249 ERPQSPRLAEFLKN 262 P+S RL +F+ + Sbjct: 269 GAPKSERLKKFISS 282 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: 196 Number of extensions: 7 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: 284 Length adjustment: 25 Effective length of query: 240 Effective length of database: 259 Effective search space: 62160 Effective search space used: 62160 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