Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_068463382.1 APY04_RS13115 urea ABC transporter ATP-binding subunit UrtE
Query= TCDB::P73650 (240 letters) >NCBI__GCF_001541235.1:WP_068463382.1 Length = 232 Score = 128 bits (321), Expect = 1e-34 Identities = 71/211 (33%), Positives = 116/211 (54%), Gaps = 1/211 (0%) Query: 4 LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEII 63 +L+ D + Y IL+ ++F + G+ + V+G NG GK+T+ +TI GL + G I Sbjct: 1 MLLSFDKVSSYYGATQILRNVSFDLEQGQCLCVLGRNGVGKTTIMRTIMGLTDRTTGSIT 60 Query: 64 FKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMF 123 E I Q G+ YVPQ + TV EN+ +G F + + + +F Sbjct: 61 MGDEAIANKPPYQRAGYGIGYVPQGRGILADFTVRENILLGTFARKDSAPEIPELCLRIF 120 Query: 124 PKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAIN 183 P L + ++RAG LSGG++Q LA+ RAL + P +LLLDEP+ + P +V ++ ++ +N Sbjct: 121 PYLRENLDRRAGLLSGGQKQQLAIARALAVGPQVLLLDEPTEGIQPNIVHEIGEILRMLN 180 Query: 184 -ATGKAIILVEQNAKQALMMADRGYVLENGR 213 G ++IL EQ+ K A + D +++NGR Sbjct: 181 KELGISLILTEQHIKVARKLGDAFLMVDNGR 211 Lambda K H 0.320 0.139 0.393 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: 123 Number of extensions: 5 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: 240 Length of database: 232 Length adjustment: 23 Effective length of query: 217 Effective length of database: 209 Effective search space: 45353 Effective search space used: 45353 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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