Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_028584459.1 G494_RS0110175 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000429965.1:WP_028584459.1 Length = 404 Score = 342 bits (876), Expect = 2e-98 Identities = 188/410 (45%), Positives = 265/410 (64%), Gaps = 21/410 (5%) Query: 3 RHLKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILATIAVCSLLMFLRVLFST 62 + ++ L AL + +P+L +K+ + ++ + + + + + + R++ + Sbjct: 5 KDIRQGLLVALWFIFLTFPLLVIKINPIENSVNWRWLNMVYVGSFSFL-IYLITRMVMAR 63 Query: 63 QISAMWKSSPGLPVIPAKAS-NFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLIL 121 ++ K GL S + P ++ A+ V L++P S V+I L Sbjct: 64 KLERQKKIKLGLVKEKVAWSIKLFSQPRLYLPLLAAVAVFFLLFPGLFSTYQVNIMITAL 123 Query: 122 IYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATFG 181 +YV+LGLGLNIVVG+AGLLDLGYV FYAVGAY+YALL+ +FGL FW LPI G++ A FG Sbjct: 124 MYVVLGLGLNIVVGVAGLLDLGYVAFYAVGAYTYALLNMHFGLGFWTVLPIGGVLGAIFG 183 Query: 182 FLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERKA 241 LLG PVLRLRGDYLAIVTLGFGEIIRL L N + + GP+GISNI +P FFG+ + Sbjct: 184 ILLGIPVLRLRGDYLAIVTLGFGEIIRLILENWSSFSHGPSGISNISRPGFFGIELSLEM 243 Query: 242 AEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIA 301 + ++++Y + +L+ L +FV+NRL IGRAW AL+EDEIA Sbjct: 244 S-------------------IVYMYYLTVLMVLFTIFVVNRLQDSRIGRAWFALKEDEIA 284 Query: 302 CRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMG 361 C+A+G++ KL+AF+LGA +AG AG FAA+ + P SFTF+ESAIIL IVVLGGMG Sbjct: 285 CQAMGIDKMKTKLTAFSLGATWAGMAGVMFAAKTTFINPASFTFLESAIILCIVVLGGMG 344 Query: 362 SQLGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQR 411 S +GVI+ A+V+IL+PE +R FS+YRML FGA++V+MMI+RPQG++ R Sbjct: 345 SIVGVIVGALVLILMPEYLRAFSDYRMLAFGAILVVMMIFRPQGIIATLR 394 Lambda K H 0.331 0.145 0.439 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: 565 Number of extensions: 29 Number of successful extensions: 3 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: 418 Length of database: 404 Length adjustment: 31 Effective length of query: 387 Effective length of database: 373 Effective search space: 144351 Effective search space used: 144351 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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