Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_110804439.1 C8J30_RS03990 LPS export ABC transporter ATP-binding protein
Query= TCDB::P73650 (240 letters) >NCBI__GCF_003217355.1:WP_110804439.1 Length = 252 Score = 129 bits (324), Expect = 5e-35 Identities = 70/218 (32%), Positives = 117/218 (53%), Gaps = 2/218 (0%) Query: 20 ILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQIVR 79 +L+ ++ + GE+V ++GPNG+GK+T TI GL+ P G + G + TG+ + R Sbjct: 29 VLRDVSLRLERGEVVALLGPNGSGKTTCFYTIAGLVAPDAGRVSIDGIDATGMPMYRRAR 88 Query: 80 RGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFPKLA--QRRNQRAGTL 137 G+ Y+PQ ++F LTV +N+ + ++R+ + A R A L Sbjct: 89 LGIGYLPQEASIFRGLTVEQNIMAVLEIAVADPHHRRERLEELLGDFAITHLRQAPALAL 148 Query: 138 SGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATGKAIILVEQNAK 197 SGGER+ + + R L DP LLLDEP A + PI V ++ A + + G +++ + N + Sbjct: 149 SGGERRRVEIARCLAADPKYLLLDEPFAGVDPIAVAEIRALVSHLKERGIGVLITDHNVR 208 Query: 198 QALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235 + L + DR Y+L +GR + G ++ D V +YLG Sbjct: 209 ETLEIVDRAYILHDGRVLMSGRTDEVVQDENVRRVYLG 246 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: 143 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: 252 Length adjustment: 24 Effective length of query: 216 Effective length of database: 228 Effective search space: 49248 Effective search space used: 49248 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 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