Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Miya:8499890 Length = 350 Score = 243 bits (619), Expect = 8e-69 Identities = 147/360 (40%), Positives = 212/360 (58%), Gaps = 28/360 (7%) Query: 1 MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60 M+ ++L V + +GDV+ + +++ +++QG ++V +GPSGCGKST LR+IAGLE +T G + Sbjct: 1 MSAIQLLNVSRHWGDVRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60 Query: 61 EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120 I V +PPAQR +AMVFQSYAL+PH+TVREN+ F L + K +AE + + A + Sbjct: 61 MIGERDVTHLPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRLTRAVDI 120 Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180 L L L R P LSGGQ+QRVA+GR++V + V L DEPLSNLDA LR R EI L+ Sbjct: 121 LGLSALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMRREIRALQ 180 Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240 + + TMVYVTHDQ EAM++A RI+++ GG I Q +P ELY +P F FIG+P M Sbjct: 181 QTL-GMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNFIGTPPM 239 Query: 241 NLL-----PGKIIGTGAQT-TVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPG 294 NL+ G + G+++ TV + D +DY +G+RPE + P Sbjct: 240 NLVRLDDARGSVCVAGSRSGTVSVVDS----ADYV-----------LGIRPEH-IRIVPE 283 Query: 295 GDYVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354 G + V E LG ++L GE+ ++ + G+ G L +H+F Sbjct: 284 G---WRAVVESVEYLGSGSVLGCRV-GGEELSV-VVDGVPTIAVGAEIYLHCPDEHIHIF 338 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: 325 Number of extensions: 14 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: 373 Length of database: 350 Length adjustment: 29 Effective length of query: 344 Effective length of database: 321 Effective search space: 110424 Effective search space used: 110424 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