Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate GFF1118 HP15_1096 branched-chain amino acid ABC transporter, ATP-binding protein
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__Marino:GFF1118 Length = 237 Score = 171 bits (434), Expect = 9e-48 Identities = 94/226 (41%), Positives = 141/226 (62%), Gaps = 1/226 (0%) Query: 1 MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60 +L+V ++T YG L + +G G+ +SL+G NG GK+T L +I G R G + F Sbjct: 5 LLEVKNLNTLYGRSHILHDLSFRLGKGQSMSLMGRNGMGKTTTLKSILGIVPPRSGHVHF 64 Query: 61 EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANELERVLTLF 120 +G+DI+++PT++ +R IA PEGR IF ++V E+LQM + G + + ERV+ F Sbjct: 65 DGEDISKLPTWKRMRRDIAYVPEGRGIFHNLTVKEHLQMAARPDSNGKTSWDFERVMDTF 124 Query: 121 PRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDIN 180 PRL+ER+S +SGGEQQMLAIGRAL++ PRL++LDE + GLAPL+ I++ + I Sbjct: 125 PRLQERLSNLGTELSGGEQQMLAIGRALVTNPRLMILDEATEGLAPLIRADIWKVIATI- 183 Query: 181 REQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEE 226 RE ++ +V++N KL V+V GK+ G+ EL N E Sbjct: 184 RESGISTLVVDKNIKALKKLCDYHVVIVKGKIHFDGSSKELDENLE 229 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: 154 Number of extensions: 6 Number of successful extensions: 1 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