Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_090447139.1 BLS63_RS17880 maltose/maltodextrin ABC transporter ATP-binding protein MalK
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_900100495.1:WP_090447139.1 Length = 371 Score = 290 bits (742), Expect = 5e-83 Identities = 155/346 (44%), Positives = 225/346 (65%), Gaps = 8/346 (2%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA++ LRN+ K+YG + I+L I+DGEF++ VGPSGCGKSTL+ IAGLE IS G Sbjct: 1 MASVTLRNICKSYGDIA--ITRQIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDISSG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 +L+ + ++ + P +R + MVFQSYALYP M+V +N+AFGLK+ K+ I +V VS Sbjct: 59 DLLIGEQRVNDLPPMERSVGMVFQSYALYPHMTVAENMAFGLKLAKVDKGAIRRKVEEVS 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++LQ++ LL RKP LSGGQ+QRVA+GR + R PK++LFDEPLSNLDA LRV+MR E+ Sbjct: 119 RILQLDQLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAALRVQMRIEISR 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +HQRL++T +YVTHDQ+EAMT+ DK+ V+ G I Q G P ++Y+ P N FVA F+GSP Sbjct: 179 LHQRLRSTMIYVTHDQVEAMTMADKIVVLNAGQIAQVGQPLELYHYPRNQFVAGFLGSPQ 238 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANG 300 MNF+ ++ + + G R ++ + + D E+ LG+RPE + A +A+ Sbjct: 239 MNFLKVKALGASSEAVEIEMPGGYRMQVLVDGSEVQAGD-ELTLGVRPEHFVDAE-QADF 296 Query: 301 LPTIRAEVQVTEPTGPDTLVFVNLN--DTKVCCRLAPDVAPAVGET 344 ++ V E G L++++L D + R + AV +T Sbjct: 297 --AFYGQIGVAERLGDHNLIYLSLEGVDDMITLRSDGNRKVAVSQT 340 Lambda K H 0.319 0.138 0.393 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: 396 Number of extensions: 10 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: 386 Length of database: 371 Length adjustment: 30 Effective length of query: 356 Effective length of database: 341 Effective search space: 121396 Effective search space used: 121396 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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