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_058929181.1 AU252_RS01290 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_001484605.1:WP_058929181.1 Length = 239 Score = 153 bits (386), Expect = 3e-42 Identities = 86/221 (38%), Positives = 131/221 (59%), Gaps = 2/221 (0%) Query: 11 LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70 LL V ++ Y + + GV+ V GE V + G NGAGKST K I G + +G + Sbjct: 10 LLAVRDLVVNY-GPIRAVSGVSIGVHRGETVVLCGANGAGKSTTIKAIMGSVPASSGSVH 68 Query: 71 FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAF-IRNDSLQPLKDKIFAM 129 G+ I + + R G+ P+ VF +++VEEN+ +GA ++ +++F Sbjct: 69 LDGQPITTVSAALRARRGIRLSPEGRQVFATMTVEENIRIGAHQLKATDRNTRVEELFDT 128 Query: 130 FPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQI 189 FP L++RRR RAG LSGG++Q++AMG+A+ P LL+LDEP L+PI + V + ++ + Sbjct: 129 FPLLAERRRSRAGDLSGGQQQIVAMGRAMASRPRLLLLDEPFLGLAPIWIASVSDAIRTV 188 Query: 190 NQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQEL 230 GTA+++ EQ AR ALE+ADRGYVL+ G A G E+ Sbjct: 189 QAAGTALLISEQMARPALELADRGYVLKHGSIARRGTADEV 229 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: 152 Number of extensions: 7 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: 247 Length of database: 239 Length adjustment: 23 Effective length of query: 224 Effective length of database: 216 Effective search space: 48384 Effective search space used: 48384 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