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_013010205.1 DACET_RS04500 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_000025725.1:WP_013010205.1 Length = 262 Score = 107 bits (266), Expect = 3e-28 Identities = 72/244 (29%), Positives = 122/244 (50%), Gaps = 35/244 (14%) Query: 28 LQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKI---TFKGK--NIAGLKSN 82 + V+ V+ E+V +IGPNGAGK+T I G+ P G I T G + GLK N Sbjct: 20 VDSVDLYVDKQEIVALIGPNGAGKTTFFNCITGIYNPSKGDIKALTHSGAVARLNGLKPN 79 Query: 83 QIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMFPRLSDRRRQR-- 140 ++ G+ Q +FP+++V EN+ +G R +K K+ R R + Sbjct: 80 RVTERGLARTFQNIRLFPNMTVLENVMIGKHCR------MKAKVLGALFRDKKTRAEELK 133 Query: 141 ---------------------AGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILV 179 A L G+++ L + +AL EPSLL+LDEP+A ++P Sbjct: 134 AATESYEILEKMGLEKFSDEMACNLPYGDQRKLEIARALATEPSLLLLDEPAAGMNPFET 193 Query: 180 TQVFEQVKQI-NQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAE 238 ++ ++QI +QE +I+L+E + + + +++R YV++ G+ G E+ +P+V + Sbjct: 194 VELTNLIRQIRDQEKISILLIEHDMKLVMNLSERIYVMDHGQKIAEGTPIEIRNNPEVIK 253 Query: 239 LYLG 242 YLG Sbjct: 254 AYLG 257 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: 127 Number of extensions: 8 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: 262 Length adjustment: 24 Effective length of query: 223 Effective length of database: 238 Effective search space: 53074 Effective search space used: 53074 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 Sep 24 2021. 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