Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate WP_035136158.1 Q763_RS16555 ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_000769915.1:WP_035136158.1 Length = 234 Score = 121 bits (303), Expect = 2e-32 Identities = 69/204 (33%), Positives = 114/204 (55%), Gaps = 9/204 (4%) Query: 4 LKLDNIYK--RYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGN 61 +K++N+ K R + ++ + ++++ EF+ +G SGCGKST L ++ L+ + G+ Sbjct: 2 IKIENLSKVFRTEEVETKALNDISIEVKKGEFVTIMGASGCGKSTLLNIVGLLDSASGGS 61 Query: 62 LYIDDKLMNDASPKDR------DIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKR 115 + D+ +N S ++ +I VFQN+ L +SVY+N+ L + KR Sbjct: 62 YKLLDREINGLSESEKAKVRKENIGFVFQNFNLIDELSVYDNIELPLIYNNVPSGERKKR 121 Query: 116 VHEAAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMR 175 V E AE LG++ L+ P LSGGQ+QR A+ RA+V + K+ L DEP NLD+K + Sbjct: 122 VEEIAERLGISHRLKHYPQQLSGGQQQRAAVARALVNNPKIILADEPTGNLDSKNGNEVM 181 Query: 176 AEIAKIHRRIGATTIYVTHDQTEA 199 + +H GAT + VTH + +A Sbjct: 182 ELLTDLHAN-GATILMVTHSEYDA 204 Lambda K H 0.318 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: 218 Number of extensions: 13 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: 377 Length of database: 234 Length adjustment: 26 Effective length of query: 351 Effective length of database: 208 Effective search space: 73008 Effective search space used: 73008 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 (21.7 bits) S2: 48 (23.1 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