Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_027722304.1 H589_RS0112350 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000425265.1:WP_027722304.1 Length = 407 Score = 358 bits (918), Expect = e-103 Identities = 202/412 (49%), Positives = 266/412 (64%), Gaps = 20/412 (4%) Query: 5 LKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILATIAVCSLLMFLRVLFSTQI 64 LK ++ ++L + P++G+ + + ++ H + AV L R L + + Sbjct: 4 LKKSILASLWFMFLTLPIMGVFVNTIDKSVTWH-LDRVLYVGAAVFVLSFVWRFLLNRKE 62 Query: 65 SAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLILIYV 124 M + +S LT P ++ LIV A+ +P S V+I LIYV Sbjct: 63 HGMQQEEQSNEEKVTFSSKLLTNPKFYYPLLAVLIVFAICFPKLFSMYQVNIMISALIYV 122 Query: 125 MLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATFGFLL 184 +LGLGLNIVVGLAGLLDLG+V FYAVGAYSYALL+ Y+G+SFWI LP+ ++ AT G LL Sbjct: 123 VLGLGLNIVVGLAGLLDLGFVAFYAVGAYSYALLNLYWGVSFWIALPVGALLGATCGLLL 182 Query: 185 GFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERKAAEG 244 GFPVLRLRGDYLAIVTLGFGEIIRL L N + T GP+GI+NI +P FFGL G Sbjct: 183 GFPVLRLRGDYLAIVTLGFGEIIRLVLENWGEFTHGPSGIANIPRPDFFGL------VSG 236 Query: 245 LQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIACRA 304 L + F+Y + L+L + +FV++RL IGRAW+ALREDEIAC+A Sbjct: 237 LS-------------GSIYFMYYLMLVLVVFTIFVVSRLKNSRIGRAWQALREDEIACQA 283 Query: 305 LGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQL 364 +G++ KL AF+LGA +AG G FAA+ + P SFTF+ESAIIL+IVVLGGMGS L Sbjct: 284 MGIDKMKTKLLAFSLGATWAGMVGVVFAAKTSFINPASFTFLESAIILSIVVLGGMGSTL 343 Query: 365 GVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMEL 416 GVIL A V+ LLPE +R+FSEYRML+FGA MVL+M++RPQGL+ R +++ Sbjct: 344 GVILGAFVLSLLPEYLRDFSEYRMLVFGATMVLVMVFRPQGLIRDVRKKIDI 395 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: 557 Number of extensions: 29 Number of successful extensions: 4 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: 407 Length adjustment: 31 Effective length of query: 387 Effective length of database: 376 Effective search space: 145512 Effective search space used: 145512 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