Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AZOBR_RS32410 AZOBR_RS32410 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__azobra:AZOBR_RS32410 Length = 355 Score = 186 bits (471), Expect = 1e-51 Identities = 109/334 (32%), Positives = 180/334 (53%), Gaps = 45/334 (13%) Query: 12 AVALLVLPLILQSFGNAWV-RIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYL 70 AVA +P + G++++ +IA +++V+L+ LN V G AGLL +G+ AFY +GAY Sbjct: 36 AVAFGAVPAAIVGTGSSYLAQIAITTMIFVILSASLNHVTGTAGLLSIGHAAFYGIGAYA 95 Query: 71 FALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAI 130 AL+++ L + +P A L+AA FG ++ PT++L Y A+ Sbjct: 96 AALLSTK----------------LGLPFIVTLPAAGLIAALFGFLVALPTMRLVSIYFAV 139 Query: 131 VTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYY 190 TLG GE+I + L N V++T GP G+ I + E+FG+ +++ Y Sbjct: 140 ATLGIGEMIYVVLLNW---VDVTRGPMGIRGIPPI-----------ELFGWQADTLLTRY 185 Query: 191 YLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGV 250 V+ V V + +RL S G A A+RED+ A +MGIN +K+ +F + F G+ Sbjct: 186 LAVAVIAVACVWVLHRLTHSYYGNALRALREDDQCADSMGINVERLKIESFVVATFFAGI 245 Query: 251 SGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGP 310 +GA+ +++P++F MES++I+AMVV+GG+G +PG ++GA+ + LPE LR Sbjct: 246 AGALLAHTSAYIAPDNFRFMESILILAMVVVGGLGSLPGAVVGALFMIVLPEALR----- 300 Query: 311 LQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344 D R + + M + +LL P+G+ Sbjct: 301 ---------DIGDYRMIAVGATMFLSILLLPKGM 325 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: 336 Number of extensions: 16 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 358 Length of database: 355 Length adjustment: 29 Effective length of query: 329 Effective length of database: 326 Effective search space: 107254 Effective search space used: 107254 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: 49 (23.5 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