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_058929664.1 AU252_RS04340 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_001484605.1:WP_058929664.1 Length = 257 Score = 259 bits (663), Expect = 3e-74 Identities = 125/241 (51%), Positives = 178/241 (73%) Query: 2 SGSAQNFTPLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGL 61 +GSA +++V N+ AGY+ V+IL G N GEL+ +IGPNGAGKSTL K +FGL Sbjct: 10 AGSAATDDSVVKVTNLVAGYLPGVNILNGCNIEARKGELIGIIGPNGAGKSTLLKAMFGL 69 Query: 62 LTPHTGKITFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQP 121 + H+G + +G++I GLK+N++V +G+ +VPQ NVF +L++EEN++MG F R Sbjct: 70 VKVHSGTVVVRGQDITGLKANKLVTMGVGFVPQNNNVFATLTIEENMQMGMFQRPKDFAE 129 Query: 122 LKDKIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQ 181 D + ++FP L RR QRAG+LSGGERQM+AMG+ALM+EP++L+LDEPSA LSP+ + Sbjct: 130 RFDFVTSLFPELGKRRAQRAGSLSGGERQMVAMGRALMMEPAVLLLDEPSAGLSPVKQDE 189 Query: 182 VFEQVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYL 241 F +V +IN+ G ++I+VEQNAR+ L++ DR YVL+ GRDA +G G+EL+ DPKV +LYL Sbjct: 190 TFLRVHEINRAGVSVIMVEQNARRCLQICDRAYVLDQGRDAYTGTGRELMKDPKVIQLYL 249 Query: 242 G 242 G Sbjct: 250 G 250 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: 205 Number of extensions: 7 Number of successful extensions: 1 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: 257 Length adjustment: 24 Effective length of query: 223 Effective length of database: 233 Effective search space: 51959 Effective search space used: 51959 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