Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF1302 (334 letters) >NCBI__GCF_000016765.1:WP_041378948.1 Length = 252 Score = 156 bits (394), Expect = 6e-43 Identities = 85/212 (40%), Positives = 120/212 (56%), Gaps = 3/212 (1%) Query: 4 IKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIRID 63 I + V K++ V+ + LTIE G F VG SG GK+TLL+ I L +I +GTI I+ Sbjct: 2 ISFDHVGKHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIE 61 Query: 64 GEDATNIPPA--KRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAAL 121 G D P A +R + VFQ L+PHMSV +N+A ++ G+P +E+ R+ + Sbjct: 62 GRDVAAQPVAELRRRIGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLDLV 121 Query: 122 NL-TDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELH 180 L D+ +RRP QLSGGQ QRV RA+ PA L DEP LD R + LH Sbjct: 122 ALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALH 181 Query: 181 KRLATTMIYVTHDQVEAMTMADKIVVLQAGVI 212 + + T + VTHD EA+ +AD+++V+ G I Sbjct: 182 EAMGLTSLIVTHDMAEALLLADRVIVIGEGRI 213 Lambda K H 0.320 0.138 0.400 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: 185 Number of extensions: 6 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: 334 Length of database: 252 Length adjustment: 26 Effective length of query: 308 Effective length of database: 226 Effective search space: 69608 Effective search space used: 69608 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