Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD
Query= reanno::Smeli:SM_b21216 (360 letters) >NCBI__GCF_900141795.1:WP_074200832.1 Length = 227 Score = 119 bits (297), Expect = 1e-31 Identities = 84/223 (37%), Positives = 121/223 (54%), Gaps = 19/223 (8%) Query: 4 LEIRNIRKRY----GEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGD 59 LE RN+ K Y E LKG+ + L E + ++GSSG GKSTLL+++ GL P+ G+ Sbjct: 6 LEGRNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGE 65 Query: 60 ILIGER--SVLGVHPK----DRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKA 113 +L+ + S LG + +R + V+Q + L P L+ N+ L +RR E + Sbjct: 66 VLLLGQPFSKLGEAARGRLRNRHMGFVYQFHHLLPELTAEENVMMPLLIRR----ESEAT 121 Query: 114 VRDTA-RLLQIENLLDR---KPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLR 169 RD A LL L R KPS+LSGG+RQRVA+ RALV P L DEP NLD++ Sbjct: 122 ARDKALALLDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSA 181 Query: 170 MEMRTELKRLHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRI 212 ++ + + L+Q T ++ VTHD + R +RDG I Sbjct: 182 EQVLSLMDDLNQRFGTALLVVTHD-VNIAARMDRTLTLRDGMI 223 Lambda K H 0.320 0.136 0.385 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: 194 Number of extensions: 10 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: 360 Length of database: 227 Length adjustment: 26 Effective length of query: 334 Effective length of database: 201 Effective search space: 67134 Effective search space used: 67134 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: 47 (22.7 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