Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD
Query= TCDB::P73650 (240 letters) >NCBI__GCF_900141795.1:WP_074200832.1 Length = 227 Score = 100 bits (248), Expect = 3e-26 Identities = 64/208 (30%), Positives = 111/208 (53%), Gaps = 7/208 (3%) Query: 16 ADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGS- 74 A+ P+L+G++ + E V ++G +G+GKSTL + GL P+ GE++ G+ + LG Sbjct: 20 AETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGEVLLLGQPFSKLGEA 79 Query: 75 --DQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFPK--LAQRR 130 ++ R M +V Q ++ LT EN+ M + + T +D+ + L++R Sbjct: 80 ARGRLRNRHMGFVYQFHHLLPELTAEENVMMPLLIRRESEATARDKALALLDAVGLSRRT 139 Query: 131 NQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINAT-GKAI 189 + LSGGERQ +A+ RAL+ +PD +L DEP+ L + V + + +N G A+ Sbjct: 140 AHKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVLSLMDDLNQRFGTAL 199 Query: 190 ILVEQNAKQALMMADRGYVLENGRDKLE 217 ++V + A M DR L +G ++E Sbjct: 200 LVVTHDVNIAARM-DRTLTLRDGMIRVE 226 Lambda K H 0.320 0.139 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: 90 Number of extensions: 4 Number of successful extensions: 2 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: 240 Length of database: 227 Length adjustment: 23 Effective length of query: 217 Effective length of database: 204 Effective search space: 44268 Effective search space used: 44268 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: 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