Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_900141795.1:WP_074200832.1 Length = 227 Score = 100 bits (248), Expect = 3e-26 Identities = 68/202 (33%), Positives = 104/202 (51%), Gaps = 7/202 (3%) Query: 24 DVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKNIAGLKSNQ 83 + +L+GV+ + E V ++G +G+GKSTL + GL P G++ G+ + L Sbjct: 21 ETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGEVLLLGQPFSKLGEAA 80 Query: 84 IVRLG---MCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMFPR--LSDRRR 138 RL M +V Q ++ P L+ EEN+ M IR +S +DK A+ LS R Sbjct: 81 RGRLRNRHMGFVYQFHHLLPELTAEENVMMPLLIRRESEATARDKALALLDAVGLSRRTA 140 Query: 139 QRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQE-GTAII 197 + LSGGERQ +A+ +AL+ EP ++ DEP+ L QV + +NQ GTA++ Sbjct: 141 HKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVLSLMDDLNQRFGTALL 200 Query: 198 LVEQNARKALEMADRGYVLESG 219 +V + A M DR L G Sbjct: 201 VVTHDVNIAARM-DRTLTLRDG 221 Lambda K H 0.317 0.136 0.377 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: 121 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: 247 Length of database: 227 Length adjustment: 23 Effective length of query: 224 Effective length of database: 204 Effective search space: 45696 Effective search space used: 45696 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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