Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD
Query= reanno::Smeli:SMc02121 (258 letters) >NCBI__GCF_900141795.1:WP_074200832.1 Length = 227 Score = 110 bits (274), Expect = 3e-29 Identities = 72/224 (32%), Positives = 119/224 (53%), Gaps = 17/224 (7%) Query: 19 IEITNMNKWYGD----FHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGK 74 +E N+ K Y D VL+ ++L + R ER+ + G SGSGKST++ + L+ G+ Sbjct: 6 LEGRNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGE 65 Query: 75 IVVDGIELTNDLKKIDEV------RREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKK 128 +++ G K+ E R +G V+Q +L P LT EN + P+ +R+ + Sbjct: 66 VLLLG----QPFSKLGEAARGRLRNRHMGFVYQFHHLLPELTAEEN-VMMPLLIRRESEA 120 Query: 129 EAEQVAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEM 188 A A+ L+ V + + P +LSGG++QRVA+AR+L P +L DEPT LD Sbjct: 121 TARDKALALLDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRS 180 Query: 189 VKEVLDTMVGLAEE-GMTMICVTHEMGFARQVANRVIFMDQGQI 231 ++VL M L + G ++ VTH++ A ++ +R + + G I Sbjct: 181 AEQVLSLMDDLNQRFGTALLVVTHDVNIAARM-DRTLTLRDGMI 223 Lambda K H 0.322 0.136 0.397 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: 133 Number of extensions: 12 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: 258 Length of database: 227 Length adjustment: 23 Effective length of query: 235 Effective length of database: 204 Effective search space: 47940 Effective search space used: 47940 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 (21.9 bits) S2: 46 (22.3 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