Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_023434295.1 N177_RS20200 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000496075.1:WP_023434295.1 Length = 441 Score = 256 bits (653), Expect = 1e-72 Identities = 154/346 (44%), Positives = 209/346 (60%), Gaps = 43/346 (12%) Query: 9 IIGAVALLVLPLI-LQSFGNAWVR-IADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAV 66 IIG +AL V L+ F + +V ++ + L Y++L GLNIVVG AGLLDLGYVAFYA+ Sbjct: 103 IIGPLALAVALLLPALPFSDRYVMDLSIMVLTYIMLGWGLNIVVGLAGLLDLGYVAFYAI 162 Query: 67 GAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGD 126 GAY FAL+A+ H F WI +P+A +LAAF+G +LG P L+LRGD Sbjct: 163 GAYSFALLAT-HFDLGF---------------WICLPLAGILAAFWGVILGFPVLRLRGD 206 Query: 127 YLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKR-----LEVFGF 181 YLAIVTL FGEIIR+ L N T GP G+ I +FGL+ +R E FG Sbjct: 207 YLAIVTLAFGEIIRVVLLNW---YEFTGGPNGILGIPDPTLFGLEFARRGDNTFHEFFGL 263 Query: 182 DINS---VTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKL 238 +S + YY+ L L +++ + RL+ +GRAW A+REDEIA +++GINT N KL Sbjct: 264 SYSSMHKIIFLYYIILCLALITNFVTLRLRRLPVGRAWEALREDEIACRSLGINTTNTKL 323 Query: 239 LAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLS 298 AF +GA FGG +G+ F QGF+SPESF+ +ES +I+A+VVLGG+G GV++ A+++ Sbjct: 324 TAFAIGAMFGGFAGSFFATRQGFISPESFTFIESALILAIVVLGGLGSQVGVVIAAIVMM 383 Query: 299 ALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344 E R + R L+ LAM+ IM+ RPRGL Sbjct: 384 GGFEYFR--------------EFEQYRMLIFGLAMVFIMVWRPRGL 415 Lambda K H 0.328 0.144 0.430 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: 414 Number of extensions: 16 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: 358 Length of database: 441 Length adjustment: 31 Effective length of query: 327 Effective length of database: 410 Effective search space: 134070 Effective search space used: 134070 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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