Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_017358586.1 BA79_RS12600 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= TCDB::P73650 (240 letters) >NCBI__GCF_000691145.1:WP_017358586.1 Length = 421 Score = 101 bits (252), Expect = 2e-26 Identities = 63/209 (30%), Positives = 111/209 (53%), Gaps = 6/209 (2%) Query: 25 NFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQ---IVRRG 81 NF + GE+ ++G +G+GKSTL + + L+ P+ GEI G+ IT + DQ + R+ Sbjct: 53 NFDVYDGEIFVIMGLSGSGKSTLVRLLNRLIEPTSGEIYIDGDMITNMSKDQLREVRRKK 112 Query: 82 MCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFPKLAQR--RNQRAGTLSG 139 + V Q +F T+ EN + G L + + + + Q LSG Sbjct: 113 ISMVFQNFALFPHRTILENTEYGLELQGVEKEQRRSKALESLKLVGLEGFEEQYPNQLSG 172 Query: 140 GERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAIN-ATGKAIILVEQNAKQ 198 G +Q + + RAL DPD+LL+DE +AL P++ KD+ ++ ++ + GK II + + + Sbjct: 173 GMQQRVGLARALANDPDILLMDEAFSALDPLIRKDMQDELLELHTSVGKTIIFITHDLDE 232 Query: 199 ALMMADRGYVLENGRDKLEGSGQSLLNDP 227 AL + DR ++++G G+ + +L +P Sbjct: 233 ALRIGDRIVLMKDGNIVQIGTPEEILMNP 261 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: 164 Number of extensions: 8 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: 421 Length adjustment: 27 Effective length of query: 213 Effective length of database: 394 Effective search space: 83922 Effective search space used: 83922 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: 48 (23.1 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