Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 8500849 DvMF_1587 ABC transporter related (RefSeq)
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Miya:8500849 Length = 366 Score = 202 bits (514), Expect = 1e-56 Identities = 130/322 (40%), Positives = 181/322 (56%), Gaps = 22/322 (6%) Query: 1 MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60 MAD+ L G+ KAYG VL ++L + GE +GPSGCGK+ LLR+IAG E GT+ Sbjct: 1 MADITLAGIGKAYGAHAVLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAGTI 60 Query: 61 EIDGTVVND------VPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAV 114 I G V+D VPP R + +VFQ YA++PHM+V +N+ + LK+A AE V Sbjct: 61 SIGGEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTRQV 120 Query: 115 EAAAEKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRL 174 E + L +R+P LSGGQ+QRVA+ R++V P + L DEPL NLDA LR R Sbjct: 121 LETVEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEMRF 180 Query: 175 EIAQLKEAMPESTMVYVTHDQVEAMTLATRIVVL-AGGGIAQVGSPLELYEKPENEFVAQ 233 EI +L+ + T++YVTHDQ A+ ++ R+ ++ G I QVG+P E++E+P +EFV + Sbjct: 181 EIKELQRTL-GITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVFR 239 Query: 234 FIGSPKMNLLPGKIIGTGAQTTVEMTDGGRAVSDY--PSDDSLMGAAVNVGVRPEDMVEA 291 F+G N LP + G + GG + P D+ A G RP D V Sbjct: 240 FMG--VANFLPARRRGMAM-----LAAGGEQPVPWGLPDGDAEHWMA---GFRPSD-VRL 288 Query: 292 APGGDYVFEGKVAITEALGEVT 313 A GD + G V LG +T Sbjct: 289 ARQGDGL-RGTVRRASFLGAMT 309 Lambda K H 0.316 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: 370 Number of extensions: 27 Number of successful extensions: 4 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: 373 Length of database: 366 Length adjustment: 30 Effective length of query: 343 Effective length of database: 336 Effective search space: 115248 Effective search space used: 115248 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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