Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_023434295.1 N177_RS20200 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:G8ALI9 (505 letters) >NCBI__GCF_000496075.1:WP_023434295.1 Length = 441 Score = 493 bits (1270), Expect = e-144 Identities = 262/482 (54%), Positives = 328/482 (68%), Gaps = 50/482 (10%) Query: 4 ISMSSPRAIAWPSILKEAAMTAFVALLLTIPLVGLRTVDRPTGLGLETRWNEVAAAVGLV 63 ++ +SP ++K+AA +A +AL L P++GL+TV GLGL RW++V Sbjct: 1 MATTSPSRRPAAELVKDAAYSALIALALAAPIIGLQTVTARGGLGLNARWDDV------- 53 Query: 64 FLGRLGLCLIREGHAVTVLVLAAAATAAGFFIAMPTEALRVILIAGGAVIAIRAVLAIRT 123 F I + A R++L + Sbjct: 54 -----------------------------FLIVLAVFAGRLLL---------NFTIWRHQ 75 Query: 124 GRSKLSQAERDKRMDHIAAQVQHA-SRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTY 182 G + Q + A+ H S+ +GP+A+ VAL P P +DR ++D+ I++LTY Sbjct: 76 GARPIGQKWFQRAGGRPFARHGHTLSKIIGPLALAVALLLPALPFSDRYVMDLSIMVLTY 135 Query: 183 IMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVL 242 IMLGWGLNIVVGLAGLLDLGYVAFYA+GAYS+ALLA +F FW+CLPLAG LAA GV+ Sbjct: 136 IMLGWGLNIVVGLAGLLDLGYVAFYAIGAYSFALLATHFDLGFWICLPLAGILAAFWGVI 195 Query: 243 LGFPVLRLRGDYFAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPA 302 LGFPVLRLRGDY AIVTL FGEIIR++L+NWY+FTGGPNGI GIP P+ FG+ +F R Sbjct: 196 LGFPVLRLRGDYLAIVTLAFGEIIRVVLLNWYEFTGGPNGILGIPDPTLFGL-EFAR--- 251 Query: 303 EGTAAFHEMFGLEFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIAC 362 G FHE FGL +S +H+IIFLYY+IL LAL+ N T+R+R+LP+GRAWEALRED+IAC Sbjct: 252 RGDNTFHEFFGLSYSSMHKIIFLYYIILCLALITNFVTLRLRRLPVGRAWEALREDEIAC 311 Query: 363 ASLGINRTNMKLAAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGS 422 SLGIN TN KL AFAI AMFGGFAGSFFATRQGFISPESFTFIESA+ILAIVVLGG+GS Sbjct: 312 RSLGINTTNTKLTAFAIGAMFGGFAGSFFATRQGFISPESFTFIESALILAIVVLGGLGS 371 Query: 423 QIGVVVAAFLVIGLPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDPTILLHGRPKG 482 Q+GVV+AA +++G E FRE YRML FG+ MV IM+WRPRGL++ R P+++L R Sbjct: 372 QVGVVIAAIVMMGGFEYFREFEQYRMLIFGLAMVFIMVWRPRGLISTRSPSVILKERKAI 431 Query: 483 GA 484 GA Sbjct: 432 GA 433 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: 685 Number of extensions: 42 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: 2 Length of query: 505 Length of database: 441 Length adjustment: 33 Effective length of query: 472 Effective length of database: 408 Effective search space: 192576 Effective search space used: 192576 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