Align ABC transporter for L-Histidine, permease component (characterized)
to candidate RR42_RS04820 RR42_RS04820 choline ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_09615 (283 letters) >FitnessBrowser__Cup4G11:RR42_RS04820 Length = 215 Score = 112 bits (279), Expect = 9e-30 Identities = 66/184 (35%), Positives = 105/184 (57%), Gaps = 5/184 (2%) Query: 94 QTLALMLVATLISVLIGIPLGILSARSNRLRSVLMPLLDIMQTMPS---FVYLIPVLMLF 150 Q LAL+ + +++++G+PLGIL AR L + L+ L I+ T+PS F +IP+ F Sbjct: 20 QHLALVGSSVGLAIVVGVPLGILCARFRFLATPLLTLATIVLTLPSIALFGLMIPIFARF 79 Query: 151 G--LGKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVMEAINAFGANRWQQLFGVQLPLAL 208 G LG VPA+ A +Y+ P++R T + + VD + EA G WQ++ V LPLA+ Sbjct: 80 GHALGYVPAVTAVFLYSLLPIMRNTCVALANVDDGIQEAGRGIGMTTWQRMRLVDLPLAV 139 Query: 209 PSIMAGINQTTMMALSMVVIASMIGARGLGEDVLVGIQTLNVGRGLEAGLAIVILAVVID 268 P I+ G+ +M + + IA++IGA GLG +L I N+ + + + +LA+V D Sbjct: 140 PVILGGVRTAVVMNIGVATIAAIIGAGGLGVLILQAISQSNMSKLAIGAVLVSVLAIVAD 199 Query: 269 RITQ 272 Q Sbjct: 200 ACLQ 203 Lambda K H 0.328 0.142 0.429 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: 217 Number of extensions: 15 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: 283 Length of database: 215 Length adjustment: 24 Effective length of query: 259 Effective length of database: 191 Effective search space: 49469 Effective search space used: 49469 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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