Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 349829 BT0301 ATP-binding transport protein natA (Na+ ABC transporter) (NCBI ptt file)
Query= TCDB::P73650 (240 letters) >FitnessBrowser__Btheta:349829 Length = 503 Score = 67.8 bits (164), Expect = 4e-16 Identities = 46/152 (30%), Positives = 83/152 (54%), Gaps = 6/152 (3%) Query: 21 LQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQIVRR 80 L+G++F I G + ++GPNGAGKSTL + I G+ S G I G + T + +++ + Sbjct: 232 LRGVSFEIQTG-MFGLLGPNGAGKSTLMRVICGIFEQSYGSIWINGLD-TRIYREEL-QS 288 Query: 81 GMCYVPQVCNVFGSLTVAENLDMGAFLH---QGPTQTLKDRIYTMFPKLAQRRNQRAGTL 137 + ++PQ + ++T E LD A L G + + + +R++++ G+ Sbjct: 289 LIGFLPQEFGTYENMTSWEFLDYQAILKGIVDGDLRRERLDYVLKAVHMYERKDEKIGSF 348 Query: 138 SGGERQMLAMGRALMLDPDLLLLDEPSAALSP 169 SGG +Q + + L+ P +L++DEP+A L P Sbjct: 349 SGGMKQRIGIALILLHLPRILVVDEPTAGLDP 380 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: 193 Number of extensions: 5 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: 240 Length of database: 503 Length adjustment: 29 Effective length of query: 211 Effective length of database: 474 Effective search space: 100014 Effective search space used: 100014 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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