Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_090272109.1 BLU11_RS03760 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:G8ALI9 (505 letters) >NCBI__GCF_900105005.1:WP_090272109.1 Length = 418 Score = 395 bits (1014), Expect = e-114 Identities = 198/317 (62%), Positives = 243/317 (76%), Gaps = 3/317 (0%) Query: 156 VVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYA 215 + AL +PF +R +D+ L+L Y+MLG GLNIVVGLAGLLDLGYV FYAVGAY+YA Sbjct: 99 IAAALVWPF--FGNRSNIDMATLVLIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYTYA 156 Query: 216 LLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILINWYQ 275 LLA YFG FW L AG +AA+ G LLGFPVLRLRGDY AIVTLGFGEIIRI+L N Sbjct: 157 LLAMYFGIGFWTGLVAAGAMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLNNLTS 216 Query: 276 FTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILVLALV 335 T GPNGI IP+P FG+ +F+R +EG FH+ FG+EF+ +HR++FLY+L L+L L+ Sbjct: 217 LTNGPNGIGSIPKPELFGL-EFSRRASEGMQTFHDFFGIEFNSVHRVMFLYFLALLLVLL 275 Query: 336 VNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFATRQ 395 R+ ++P+GRAWEA+RED++AC SLGIN T +KL AF I A F GFAG FFA RQ Sbjct: 276 TLFVINRLLRMPVGRAWEAMREDEVACRSLGINPTAVKLNAFTIGATFAGFAGCFFAARQ 335 Query: 396 GFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRMLAFGMGM 455 GFISPESFTFIESAIILAIVVLGGMGSQ+GV++AA ++ LPE R+ +YRML FG+ M Sbjct: 336 GFISPESFTFIESAIILAIVVLGGMGSQLGVILAAIIMTLLPEVARQFDEYRMLLFGLLM 395 Query: 456 VLIMLWRPRGLLAHRDP 472 VL+M+WRP+GLL + P Sbjct: 396 VLMMIWRPQGLLPMKRP 412 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: 620 Number of extensions: 38 Number of successful extensions: 2 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: 418 Length adjustment: 33 Effective length of query: 472 Effective length of database: 385 Effective search space: 181720 Effective search space used: 181720 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: 51 (24.3 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