Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate BPHYT_RS04430 BPHYT_RS04430 amino acid ABC transporter ATPase
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__BFirm:BPHYT_RS04430 Length = 244 Score = 202 bits (513), Expect = 6e-57 Identities = 107/245 (43%), Positives = 160/245 (65%), Gaps = 10/245 (4%) Query: 1 MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60 ML + +H YG ++ L G+ I++ +V+LIG+NGAGK+T + I G R G IT Sbjct: 1 MLSIRNLHAGYGKVKVLHGISIDVPKASVVTLIGSNGAGKTTTMRAISGMIRPSAGEITM 60 Query: 61 ----EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSI----TAKP-GSFAN 111 + + I + ++ + RLG+A SPEGRR+F MSV +NL +G+ +A+P G Sbjct: 61 GVGTDAKRIDALDSHRIARLGLAHSPEGRRVFATMSVTDNLILGAFPRLTSARPRGDVKA 120 Query: 112 ELERVLTLFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQ 171 +LER + +FPRLKER Q AGT+SGGEQQMLA+ RA+M P L+LLDEPS+GLAP++V++ Sbjct: 121 DLERAIEMFPRLKERRHQLAGTLSGGEQQMLAMARAIMMNPDLVLLDEPSMGLAPILVEE 180 Query: 172 IFQAVKDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAY 231 +F+ + ++ + Q +T+ +VEQ A AL +A GYV+ NG++ G EL + V++AY Sbjct: 181 VFRIIGNL-KSQGVTMLLVEQFAAAALNVADYGYVLENGRIAAHGPATELRNDPSVKAAY 239 Query: 232 LEGGH 236 L H Sbjct: 240 LGASH 244 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: 180 Number of extensions: 7 Number of successful extensions: 4 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: 244 Length adjustment: 23 Effective length of query: 213 Effective length of database: 221 Effective search space: 47073 Effective search space used: 47073 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