Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_011939016.1 GURA_RS10785 ABC transporter ATP-binding protein
Query= TCDB::P73650 (240 letters) >NCBI__GCF_000016745.1:WP_011939016.1 Length = 250 Score = 111 bits (277), Expect = 2e-29 Identities = 72/235 (30%), Positives = 120/235 (51%), Gaps = 17/235 (7%) Query: 18 VPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQI 77 + L+ ++FSI + +IGPNGAGK+TL + G+ TP+ G ++ ++I+ L S++ Sbjct: 14 ITALEDVSFSIGKDLITGIIGPNGAGKTTLFNIVTGIYTPTSGSVLLGDKDISRLPSEKR 73 Query: 78 VRRGMCYVPQVCNVFGSLTVAENLDMG-------AFL--------HQGPTQTLKDRI--Y 120 GM Q +FG +TV EN+ +G FL H + ++D + Sbjct: 74 AYLGMVRTFQNIELFGKMTVLENVMVGLHSKSSSGFLACAFKMPWHLREERRIRDNAMRW 133 Query: 121 TMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIK 180 F +A Q A L G+ ++L + RAL L+P +LL+DEP+A L+ ++ I+ Sbjct: 134 LEFTGIADLAQQEAANLPFGKGRLLEIARALALEPKILLMDEPAAGLNSKETHELSLLIR 193 Query: 181 AINATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235 I G ++LVE + + + + D VL GR EG+ + + +P V YLG Sbjct: 194 KIREMGVTVVLVEHDMELVMDICDSIVVLNLGRKLAEGTPREIQENPEVVAAYLG 248 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: 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: 250 Length adjustment: 24 Effective length of query: 216 Effective length of database: 226 Effective search space: 48816 Effective search space used: 48816 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 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