Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein
Query= TCDB::P73650 (240 letters) >NCBI__GCF_900115975.1:WP_092484009.1 Length = 344 Score = 112 bits (280), Expect = 1e-29 Identities = 71/210 (33%), Positives = 114/210 (54%), Gaps = 6/210 (2%) Query: 21 LQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQIVRR 80 L IN + GE ++GP G GK+ + +TI G+ P +G I FK N+ L +Q R Sbjct: 16 LLDINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLATLAPEQ---R 72 Query: 81 GMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFPKLA--QRRNQRAGTLS 138 + +V Q +F LTV EN+ GA + + P + +K ++ + L N+ TLS Sbjct: 73 KVGFVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLNRHPSTLS 132 Query: 139 GGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATGKAIIL-VEQNAK 197 GGE+Q A+ RAL++ P++LLLDEP +AL P ++ ++K I+ T K L V + Sbjct: 133 GGEQQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTLHVTHDFN 192 Query: 198 QALMMADRGYVLENGRDKLEGSGQSLLNDP 227 +A+ +AD+ V+ G+ G+ Q + P Sbjct: 193 EAMYLADKIGVMHQGQIIQVGTPQEIFYKP 222 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: 183 Number of extensions: 10 Number of successful extensions: 3 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: 344 Length adjustment: 26 Effective length of query: 214 Effective length of database: 318 Effective search space: 68052 Effective search space used: 68052 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: 47 (22.7 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