Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate BPHYT_RS31755 BPHYT_RS31755 amino acid ABC transporter ATPase
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__BFirm:BPHYT_RS31755 Length = 237 Score = 229 bits (584), Expect = 4e-65 Identities = 118/233 (50%), Positives = 173/233 (74%), Gaps = 2/233 (0%) Query: 1 MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60 +LK+ G+ YG I+A+K VD+E+ G++V+LIGANGAGK+T + I G +G I + Sbjct: 4 ILKIKGLQVNYGGIQAVKNVDMEVKTGDLVTLIGANGAGKTTTMKAIAGLKPYSVGDIEY 63 Query: 61 EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGS-ITAKPGSFANELERVLTL 119 G I +PT+EL++ G+A PEGR IF RMS++EN+QMG+ + ++ER+ Sbjct: 64 MGASIKGIPTHELLKRGLAMVPEGRGIFARMSIIENMQMGAYLRDDLHGVKRDIERMFGF 123 Query: 120 FPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDI 179 FPRL+ER Q AGT+SGGEQQMLA+ RA++S+P+LLLLDEPS+GL+P++V++IF+ V+++ Sbjct: 124 FPRLEERKLQFAGTLSGGEQQMLAMARAIISKPKLLLLDEPSMGLSPIMVEKIFEVVREV 183 Query: 180 NREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232 +RE +TV +VEQNA AL+ A RGYVM +G VTMSG +++L + +VR+AYL Sbjct: 184 SRE-GITVLLVEQNARLALQAASRGYVMESGTVTMSGDASKMLDDPKVRAAYL 235 Lambda K H 0.320 0.136 0.377 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: 167 Number of extensions: 7 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: 236 Length of database: 237 Length adjustment: 23 Effective length of query: 213 Effective length of database: 214 Effective search space: 45582 Effective search space used: 45582 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