Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate SMc04140 SMc04140 ABC transporter ATP-binding protein
Query= SwissProt::P19566 (369 letters) >FitnessBrowser__Smeli:SMc04140 Length = 360 Score = 380 bits (975), Expect = e-110 Identities = 202/359 (56%), Positives = 249/359 (69%), Gaps = 2/359 (0%) Query: 3 SVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFI 62 SV L+ V K +G + V I+L I GEF VFVGPSGCGKSTLLRMIAGLE I+ G L + Sbjct: 4 SVVLQKVEKRYGALDVIHGIDLTIDPGEFAVFVGPSGCGKSTLLRMIAGLEEISGGTLML 63 Query: 63 GETRMNDIPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVMNQRVNQVAEVLQ 122 RMN++ PA RG+ MVFQSYALYPH+SV +N++FGL+ AG KK + +V + AE+LQ Sbjct: 64 DSDRMNEVAPARRGIAMVFQSYALYPHMSVYKNLAFGLETAGFKKAEIEPKVRRAAEILQ 123 Query: 123 LAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLHKR 182 + LL+RKPKALSGGQRQRVAIGR +V EPR+FL DEPLSNLDA LRVQMR+EISRLH+ Sbjct: 124 IEKLLDRKPKALSGGQRQRVAIGRAIVREPRIFLFDEPLSNLDAELRVQMRVEISRLHRD 183 Query: 183 LGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMNFL 242 LG TMIYVTHDQVEAMT+ADKIVVL++GR+ QVG PL+LY+ P +RFVAGFIGSPKMNFL Sbjct: 184 LGNTMIYVTHDQVEAMTMADKIVVLNSGRIEQVGAPLDLYNNPVNRFVAGFIGSPKMNFL 243 Query: 243 PVKVTATAIEQVQVELPNRQQIWLPVESRGVQVGANMSLGIRPEHLLPSDIADVTLEGEV 302 ++ + +E+ I LP G G +++ GIRPEHL + V Sbjct: 244 KARIADVTGSETAIEVCG-GTIRLPRRLNGATQGQDVTFGIRPEHLSAREGGIELATVNV 302 Query: 303 QVVEQLGHETQIHIQIPAIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDGSACR 361 ++VE LG ET ++ I RQ L VE G+ A+ P RCH+F DG A R Sbjct: 303 EIVENLGGETMLY-GITPDRQQLTVALEGQQKVERGSNLAVHFDPSRCHVFGADGRAMR 360 Lambda K H 0.321 0.138 0.396 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: 387 Number of extensions: 11 Number of successful extensions: 3 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: 369 Length of database: 360 Length adjustment: 29 Effective length of query: 340 Effective length of database: 331 Effective search space: 112540 Effective search space used: 112540 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