Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Miya:8499890 Length = 350 Score = 250 bits (638), Expect = 5e-71 Identities = 140/354 (39%), Positives = 208/354 (58%), Gaps = 15/354 (4%) Query: 1 MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60 M+ + L ++ + +G V + + ++++G +V +GPSGCGKST LR+IAGLE +T G + Sbjct: 1 MSAIQLLNVSRHWGDVRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60 Query: 61 FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120 I V +PP++R +AMVFQSYAL+PH+TV +N+ FG+ + + + E ++R+ A D+ Sbjct: 61 MIGERDVTHLPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRLTRAVDI 120 Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180 L L+ L R P LSGGQ+QRVA+GRA+ V L DEPLSNLDA LR R EI L Sbjct: 121 LGLSALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMRREIRALQ 180 Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240 + + TM+YVTHDQ EAM++ADRI+++ G I Q P ELY RPA F FIG+P M Sbjct: 181 QTLG-MTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNFIGTPPM 239 Query: 241 NVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEG 300 N+ + + +V +AG +S T+ V +A G+RPE +R+ + Sbjct: 240 NL----VRLDDARGSVCVAGSRSGTVSVVDSAD-----YVLGIRPEHIRIVPEG---WRA 287 Query: 301 TVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFD 354 V VE LG ++L V E + + G+ + G ++ +H+FD Sbjct: 288 VVESVEYLGSGSVLGCR--VGGEELSVVVDGVPTIAVGAEIYLHCPDEHIHIFD 339 Lambda K H 0.320 0.137 0.387 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: 303 Number of extensions: 12 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: 362 Length of database: 350 Length adjustment: 29 Effective length of query: 333 Effective length of database: 321 Effective search space: 106893 Effective search space used: 106893 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: 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