Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_045585060.1 AL072_RS29555 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:G8ALI9 (505 letters) >NCBI__GCF_001305595.1:WP_045585060.1 Length = 497 Score = 786 bits (2031), Expect = 0.0 Identities = 393/479 (82%), Positives = 430/479 (89%) Query: 10 RAIAWPSILKEAAMTAFVALLLTIPLVGLRTVDRPTGLGLETRWNEVAAAVGLVFLGRLG 69 R + W + +K+AA+ AFVALLLT+PLVGLRTVDRPTGLG+E R EV A++ LVFLGRLG Sbjct: 18 RGVDWAATIKDAALAAFVALLLTVPLVGLRTVDRPTGLGIEARPEEVVASLLLVFLGRLG 77 Query: 70 LCLIREGHAVTVLVLAAAATAAGFFIAMPTEALRVILIAGGAVIAIRAVLAIRTGRSKLS 129 L LIR+G A+ VLVLA G + MPT+ LR++L+ GG VIA+RA + + TGRSKLS Sbjct: 78 LGLIRQGMALPVLVLAVLCAGIGLVLPMPTQVLRLVLVLGGGVIALRAAMTVATGRSKLS 137 Query: 130 QAERDKRMDHIAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGL 189 QA+RD+RMD +AA+VQHASR++GP+AV +A+ P TPLADR LLDIGILLLTYIMLGWGL Sbjct: 138 QADRDRRMDRVAARVQHASRYIGPVAVAIAVVLPMTPLADRMLLDIGILLLTYIMLGWGL 197 Query: 190 NIVVGLAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLR 249 NIVVGLAGLLDLGYVAFYAVGAYSYALLAHYFG SFW+CLPLAG LAA SGVLLGFPVLR Sbjct: 198 NIVVGLAGLLDLGYVAFYAVGAYSYALLAHYFGLSFWLCLPLAGVLAAFSGVLLGFPVLR 257 Query: 250 LRGDYFAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFH 309 LRGDYFAIVTLGFGEIIRIIL+NWYQFTGGPNGISGIPRPSFFGIA+F+RTPA+G AAFH Sbjct: 258 LRGDYFAIVTLGFGEIIRIILVNWYQFTGGPNGISGIPRPSFFGIAEFSRTPADGMAAFH 317 Query: 310 EMFGLEFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINR 369 EMFGLEFSPLHRI+FLYYLIL LALVVN+FT+RVRKLPLGRAWEALREDDIACASLGINR Sbjct: 318 EMFGLEFSPLHRIVFLYYLILALALVVNVFTLRVRKLPLGRAWEALREDDIACASLGINR 377 Query: 370 TNMKLAAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVA 429 TNMKLAAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVA Sbjct: 378 TNMKLAAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVA 437 Query: 430 AFLVIGLPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDPTILLHGRPKGGAGGPA 488 LVIGLPEAFRELADYRMLAFG GMV+IMLWRPRGLLAHRDPTILLHG A G A Sbjct: 438 TLLVIGLPEAFRELADYRMLAFGAGMVVIMLWRPRGLLAHRDPTILLHGGKTPAATGAA 496 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: 908 Number of extensions: 36 Number of successful extensions: 1 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: 505 Length of database: 497 Length adjustment: 34 Effective length of query: 471 Effective length of database: 463 Effective search space: 218073 Effective search space used: 218073 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: 52 (24.6 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