Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_035136158.1 Q763_RS16555 ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_000769915.1:WP_035136158.1 Length = 234 Score = 131 bits (330), Expect = 2e-35 Identities = 72/215 (33%), Positives = 123/215 (57%), Gaps = 9/215 (4%) Query: 6 LEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIG 65 L +++T +T+ + D +++++ EF +G SGCGK+T L ++ L+ + G+ + Sbjct: 7 LSKVFRTEEVETK-ALNDISIEVKKGEFVTIMGASGCGKSTLLNIVGLLDSASGGSYKLL 65 Query: 66 DRRVNDVPPKDR------DIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEA 119 DR +N + ++ +I VFQN+ L ++VY N+ L VP E +RV+E Sbjct: 66 DREINGLSESEKAKVRKENIGFVFQNFNLIDELSVYDNIELPLIYNNVPSGERKKRVEEI 125 Query: 120 AKILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIR 179 A+ L I+H L P+ LSGGQ+QR A+ RA+V P++ L DEP NLD+K ++ + Sbjct: 126 AERLGISHRLKHYPQQLSGGQQQRAAVARALVNNPKIILADEPTGNLDSKNGNEVMELLT 185 Query: 180 KLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVI 214 LH T++ VTH + +A + + + M+DG+I Sbjct: 186 DLHAN-GATILMVTHSEYDA-SFSQKTIYMKDGMI 218 Lambda K H 0.321 0.138 0.395 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: 203 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: 384 Length of database: 234 Length adjustment: 27 Effective length of query: 357 Effective length of database: 207 Effective search space: 73899 Effective search space used: 73899 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: 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