Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_028321060.1 H567_RS0108380 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000422285.1:WP_028321060.1 Length = 349 Score = 175 bits (443), Expect = 2e-48 Identities = 114/349 (32%), Positives = 189/349 (54%), Gaps = 47/349 (13%) Query: 8 WIIGAVALLVL-PLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAV 66 W + +A LVL PL +++ ++ +A+ + +L+A+GLN++VGY G + LG+ F+A+ Sbjct: 22 WFLCLIAFLVLFPLFAKNY---YIYMANYMAINILVAVGLNLLVGYTGQISLGHAGFFAL 78 Query: 67 GAY-LFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRG 125 GAY LMA HL + +P AAL AA FG +LG P L+L G Sbjct: 79 GAYGTIILMAEVHLP-----------------FILALPAAALGAALFGFLLGLPALRLEG 121 Query: 126 DYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINS 185 YL+I TLGFG I + ++ L G +GL D V + + ++S Sbjct: 122 PYLSIATLGFGLTITQVIGRIE----LFGGRQGLHTPDLV------------IGPWHLDS 165 Query: 186 VTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGA 245 +YYL +++ V+ + + +++GRA++A+R+ ++AA+ MG+N K LAF + A Sbjct: 166 DRDFYYLLVIITVLLTLAARNIIKTKVGRAFIALRDADVAAETMGVNLTLYKTLAFAVSA 225 Query: 246 SFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLR 305 + G++G ++ F+ PE F L+ S++ +AMVV+GG+G I G I GA LLS L LR Sbjct: 226 FYTGIAGGLYAFVLRFIEPEMFGLLMSIIFLAMVVVGGLGSIFGSIAGACLLSWLDLELR 285 Query: 306 ------YVAGPLQAMTDGRLD---SAILRQLLIALAMIIIMLLRPRGLW 345 Y+ LQ ++ + ++ ++ L M++IML P G++ Sbjct: 286 NILSIPYLGEWLQVLSQSYFSITGVSNIQFIVYGLIMVLIMLFEPLGIY 334 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: 315 Number of extensions: 24 Number of successful extensions: 3 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: 349 Length adjustment: 29 Effective length of query: 329 Effective length of database: 320 Effective search space: 105280 Effective search space used: 105280 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 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