Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein
Query= BRENDA::P68187 (371 letters) >NCBI__GCF_000016765.1:WP_041378948.1 Length = 252 Score = 153 bits (386), Expect = 6e-42 Identities = 91/237 (38%), Positives = 129/237 (54%), Gaps = 9/237 (3%) Query: 4 VQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFIG 63 + +V K + V D++L I G FV VG SG GK+TLL+ I L I +G + I Sbjct: 2 ISFDHVGKHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIE 61 Query: 64 EKRMNDTPPAE--RGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEVL 121 + + P AE R +G VFQ L+PH+SVAEN++ +L G +E +R +VAE+L Sbjct: 62 GRDVAAQPVAELRRRIGYVFQGIGLFPHMSVAENVALVPRLQGVPRE---ERAARVAELL 118 Query: 122 QL----AHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEIS 177 L A +R+P LSGGQ QRV R L A P++ L+DEP LD R ++ Sbjct: 119 DLVALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYR 178 Query: 178 RLHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFI 234 LH+ +G T + VTHD EA+ LAD+++V+ GR+ P L H D + I Sbjct: 179 ALHEAMGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPRALIHGAGDPRIEAMI 235 Lambda K H 0.320 0.137 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: 203 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: 371 Length of database: 252 Length adjustment: 27 Effective length of query: 344 Effective length of database: 225 Effective search space: 77400 Effective search space used: 77400 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 Apr 09 2024. 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