Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized)
to candidate WP_047006727.1 AAW01_RS07155 ATP-binding cassette domain-containing protein
Query= reanno::WCS417:GFF2490 (367 letters) >NCBI__GCF_001010925.1:WP_047006727.1 Length = 255 Score = 154 bits (388), Expect = 3e-42 Identities = 85/221 (38%), Positives = 129/221 (58%), Gaps = 5/221 (2%) Query: 4 LKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIELD 63 L+I L K ++G + + LE+ EFV VG SG GKSTLL+ + L E EG++++D Sbjct: 9 LRIAGLSKTYDGARAVDTVSLEIGAGEFVALVGASGSGKSTLLKCVNRLVEPDEGSVQID 68 Query: 64 GRDITEVTPA--KRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARIL 121 G+D + PA +R + VFQ L+PH++V +N++ L L +++E ++ Sbjct: 69 GQDTAGLPPAESRRRIGYVFQGIGLFPHLTVAQNIALPSRLES--NALSADRIAELLALV 126 Query: 122 ELGP-LLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 EL P + +R P +LSGGQRQRV + RA+ + L DEP LD R ++ + RLH Sbjct: 127 ELEPEMAQRMPSELSGGQRQRVGVARALSSESHLLLMDEPFGALDPLTRGELGKRVRRLH 186 Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLEL 221 +L T + VTHD EA+ LA +V+V++SGRI +P L Sbjct: 187 DQLHLTTVLVTHDMAEALLLATRVLVMDSGRIVADETPAAL 227 Lambda K H 0.319 0.136 0.384 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: 367 Length of database: 255 Length adjustment: 27 Effective length of query: 340 Effective length of database: 228 Effective search space: 77520 Effective search space used: 77520 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