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_041099049.1 SUTH_RS10300 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_000828635.1:WP_041099049.1 Length = 268 Score = 188 bits (477), Expect = 1e-52 Identities = 104/245 (42%), Positives = 156/245 (63%), Gaps = 9/245 (3%) Query: 11 LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70 +LE+ N+ Y K V +L+G++ R+ G++V ++G NGAGK+T K + GLL G++T Sbjct: 5 VLEINNIEVIYNKAVQVLRGLSLRLPRGQIVALLGSNGAGKTTTLKAVSGLLALEDGEMT 64 Query: 71 -----FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKD- 124 G + A LK +++VR G+ +V + VF L+VEENL + D Sbjct: 65 RGSVVLDGVDTARLKPHELVRSGLFHVMEGRRVFEDLTVEENLVAATYALTGRRATSADF 124 Query: 125 -KIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVF 183 ++ FPRL +R+R AG LSGGE+QMLA+G+AL+ P +++LDEPS LSP+LV +F Sbjct: 125 DLVYEYFPRLHERKRGLAGYLSGGEQQMLAIGRALIARPKVMLLDEPSLGLSPLLVENIF 184 Query: 184 EQVKQINQE-GTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242 + +IN+E G +++LVEQNA AL +A GY++E+G+ I GP ++L DP V E YLG Sbjct: 185 TIIARINREQGVSMLLVEQNASVALAVAHTGYIMETGKVVIDGPAEKLAGDPDVREFYLG 244 Query: 243 -AGKG 246 AG+G Sbjct: 245 MAGEG 249 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: 196 Number of extensions: 7 Number of successful extensions: 4 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: 268 Length adjustment: 24 Effective length of query: 223 Effective length of database: 244 Effective search space: 54412 Effective search space used: 54412 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: 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