Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Pf1N1B4_1079 Lipopolysaccharide ABC transporter, ATP-binding protein LptB
Query= TCDB::P73650 (240 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1079 Length = 241 Score = 115 bits (289), Expect = 6e-31 Identities = 67/220 (30%), Positives = 121/220 (55%), Gaps = 5/220 (2%) Query: 20 ILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQIVR 79 +++ ++ SI G++V ++GPNGAGK+T I GL+ QG ++ +++ + Sbjct: 18 VVRDVSLSIDSGQIVGLLGPNGAGKTTCFYMIVGLVQADQGRVLIDDLDVSHQPMHGRAK 77 Query: 80 RGMCYVPQVCNVFGSLTVAEN----LDMGAFLHQGPTQTLKDRIYTMFPKLAQRRNQRAG 135 G+ Y+PQ ++F L+VA+N L+ L Q + + + F + R+ Sbjct: 78 AGIGYLPQEASIFRKLSVADNIMAILETRKELDQAGRRQELESLLQEF-HIHHIRDNLGM 136 Query: 136 TLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATGKAIILVEQN 195 +LSGGER+ + + RAL +P +LLDEP A + PI V D+ I + A G +++ + N Sbjct: 137 SLSGGERRRVEIARALATNPKFILLDEPFAGVDPISVGDIKQIIHHLKAKGIGVLITDHN 196 Query: 196 AKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235 ++ L + + Y++ +G+ EG ++L + LV E+YLG Sbjct: 197 VRETLDICETAYIVNDGQLIAEGDSATILANELVKEVYLG 236 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: 126 Number of extensions: 6 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: 241 Length adjustment: 23 Effective length of query: 217 Effective length of database: 218 Effective search space: 47306 Effective search space used: 47306 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 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