Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate AZOBR_RS32410 AZOBR_RS32410 branched-chain amino acid ABC transporter permease
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__azobra:AZOBR_RS32410 Length = 355 Score = 221 bits (562), Expect = 4e-62 Identities = 135/353 (38%), Positives = 188/353 (53%), Gaps = 40/353 (11%) Query: 156 VVVALAFPFTPLA-----DRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVG 210 +++A+AF P A L I I + +++L LN V G AGLL +G+ AFY +G Sbjct: 33 LLLAVAFGAVPAAIVGTGSSYLAQIAITTMIFVILSASLNHVTGTAGLLSIGHAAFYGIG 92 Query: 211 AYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIIL 270 AY+ ALL+ G F V LP AG +AA+ G L+ P +RL YFA+ TLG GE+I ++L Sbjct: 93 AYAAALLSTKLGLPFIVTLPAAGLIAALFGFLVALPTMRLVSIYFAVATLGIGEMIYVVL 152 Query: 271 INWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLIL 330 +NW T GP GI GIP FG T ++ Y + Sbjct: 153 LNWVDVTRGPMGIRGIPPIELFGWQADT-----------------------LLTRYLAVA 189 Query: 331 VLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSF 390 V+A+ R+ G A ALREDD S+GIN +K+ +F +A F G AG+ Sbjct: 190 VIAVACVWVLHRLTHSYYGNALRALREDDQCADSMGINVERLKIESFVVATFFAGIAGAL 249 Query: 391 FATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRMLA 450 A +I+P++F F+ES +ILA+VV+GG+GS G VV A +I LPEA R++ DYRM+A Sbjct: 250 LAHTSAYIAPDNFRFMESILILAMVVVGGLGSLPGAVVGALFMIVLPEALRDIGDYRMIA 309 Query: 451 FGMGMVLIMLWRPRGLLAHRDPTILLHGRPKGGAGGPAAGSAAAGGQGIAGGS 503 G M L +L P+G+LA +G A G S + G IAGG+ Sbjct: 310 VGATMFLSILLLPKGMLA------------EGTALGFVRRSFSRGWATIAGGT 350 Lambda K H 0.329 0.144 0.438 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: 449 Number of extensions: 25 Number of successful extensions: 3 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: 505 Length of database: 355 Length adjustment: 32 Effective length of query: 473 Effective length of database: 323 Effective search space: 152779 Effective search space used: 152779 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 (21.8 bits) S2: 50 (23.9 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