Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_090272109.1 BLU11_RS03760 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_900105005.1:WP_090272109.1 Length = 418 Score = 272 bits (696), Expect = 1e-77 Identities = 164/354 (46%), Positives = 218/354 (61%), Gaps = 49/354 (13%) Query: 5 KTNWIIGAVALLVLPLILQSFGN-AWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAF 63 + W A LV P FGN + + +A L L+YV+L LGLNIVVG AGLLDLGYV F Sbjct: 92 RLTWCFLIAAALVWPF----FGNRSNIDMATLVLIYVMLGLGLNIVVGLAGLLDLGYVGF 147 Query: 64 YAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKL 123 YAVGAY +AL+A F G W + A +AA FG +LG P L+L Sbjct: 148 YAVGAYTYALLAM------------YFGIGF----WTGLVAAGAMAALFGFLLGFPVLRL 191 Query: 124 RGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL------- 176 RGDYLAIVTLGFGEIIRI LNNL +LTNGP G+G I ++FGL+ +R Sbjct: 192 RGDYLAIVTLGFGEIIRILLNNL---TSLTNGPNGIGSIPKPELFGLEFSRRASEGMQTF 248 Query: 177 -EVFGFDINSV---TLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGIN 232 + FG + NSV Y+L L+LV++++ + RL +GRAW A+REDE+A +++GIN Sbjct: 249 HDFFGIEFNSVHRVMFLYFLALLLVLLTLFVINRLLRMPVGRAWEAMREDEVACRSLGIN 308 Query: 233 TRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVIL 292 +KL AF +GA+F G +G F A QGF+SPESF+ +ES +I+A+VVLGG+G GVIL Sbjct: 309 PTAVKLNAFTIGATFAGFAGCFFAARQGFISPESFTFIESAIILAIVVLGGMGSQLGVIL 368 Query: 293 GAVLLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP 346 A++++ LPEV R + D R LL L M+++M+ RP+GL P Sbjct: 369 AAIIMTLLPEVAR------------QFDE--YRMLLFGLLMVLMMIWRPQGLLP 408 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: 376 Number of extensions: 14 Number of successful extensions: 5 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: 418 Length adjustment: 30 Effective length of query: 328 Effective length of database: 388 Effective search space: 127264 Effective search space used: 127264 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