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_068463382.1 APY04_RS13115 urea ABC transporter ATP-binding subunit UrtE
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_001541235.1:WP_068463382.1 Length = 232 Score = 142 bits (357), Expect = 8e-39 Identities = 79/221 (35%), Positives = 128/221 (57%), Gaps = 2/221 (0%) Query: 11 LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70 LL + V + Y IL+ V+F +E G+ + V+G NG GK+T+ +TI GL TG IT Sbjct: 2 LLSFDKV-SSYYGATQILRNVSFDLEQGQCLCVLGRNGVGKTTIMRTIMGLTDRTTGSIT 60 Query: 71 FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMF 130 + IA Q G+ YVPQ + +V EN+ +G F R DS + + +F Sbjct: 61 MGDEAIANKPPYQRAGYGIGYVPQGRGILADFTVRENILLGTFARKDSAPEIPELCLRIF 120 Query: 131 PRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQIN 190 P L + +RAG LSGG++Q LA+ +AL + P +L+LDEP+ + P +V ++ E ++ +N Sbjct: 121 PYLRENLDRRAGLLSGGQKQQLAIARALAVGPQVLLLDEPTEGIQPNIVHEIGEILRMLN 180 Query: 191 QE-GTAIILVEQNARKALEMADRGYVLESGRDAISGPGQEL 230 +E G ++IL EQ+ + A ++ D ++++GR GP E+ Sbjct: 181 KELGISLILTEQHIKVARKLGDAFLMVDNGRVVARGPIDEM 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: 147 Number of extensions: 6 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: 232 Length adjustment: 23 Effective length of query: 224 Effective length of database: 209 Effective search space: 46816 Effective search space used: 46816 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