Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_050462656.1 AKL27_RS09910 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:G8ALI9 (505 letters) >NCBI__GCF_001189915.1:WP_050462656.1 Length = 408 Score = 400 bits (1028), Expect = e-116 Identities = 213/402 (52%), Positives = 271/402 (67%), Gaps = 4/402 (0%) Query: 77 HAVTVLVLAAAATAAGFFIAMPTEALRVILIAGGA--VIAIRAVLAIRTGRSKLSQAERD 134 +AV +L A T + + E RV+L A +IA+ AV + + LS+ + Sbjct: 7 NAVAAAILTAILTTPLLGLKLQLEGYRVVLQAHWTPVLIAVLAVFLFQLFKPALSRTTAN 66 Query: 135 KRMDHIAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVG 194 R+ + R+ + + VAL +PF R +D+ L L Y++LG GLNIVVG Sbjct: 67 IRLPALPKLQPTQQRYALMVLLAVALVWPF--FGSRGNVDVVTLALIYVVLGLGLNIVVG 124 Query: 195 LAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDY 254 AGLLDLGYV FYAVG Y+YALL YFG SFW CLPLA ++A+ G LLGFPVLRLRGDY Sbjct: 125 FAGLLDLGYVGFYAVGGYTYALLNQYFGLSFWECLPLAAGMSALFGFLLGFPVLRLRGDY 184 Query: 255 FAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGL 314 AIVTLGFGEIIR++L N TGGP+G+SGIP+P+ FGI EG FH+M GL Sbjct: 185 LAIVTLGFGEIIRLLLNNLTSLTGGPDGVSGIPKPTVFGIEMARTASVEGGTTFHDMLGL 244 Query: 315 EFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKL 374 + H +IFLY+L L+L L T R+ ++P+GRAWEALR+D+IAC SLGIN T +KL Sbjct: 245 TYQGGHMVIFLYFLGLLLVLFTYFVTSRLIRMPMGRAWEALRDDEIACRSLGINPTKIKL 304 Query: 375 AAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVI 434 +AF + A F G AGSFFA RQG ++PESFTFIESA+ILAIVVLGGMGSQ+GV++AA L+ Sbjct: 305 SAFTLGAAFAGLAGSFFAARQGLVNPESFTFIESALILAIVVLGGMGSQLGVILAAILLT 364 Query: 435 GLPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDPTILL 476 LPE R A+YRML FG+ MVL+M+WRP+GLL P + L Sbjct: 365 ILPEVARSFAEYRMLIFGLVMVLMMIWRPQGLLPATRPHVEL 406 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: 632 Number of extensions: 34 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: 408 Length adjustment: 33 Effective length of query: 472 Effective length of database: 375 Effective search space: 177000 Effective search space used: 177000 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 Apr 09 2024. 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