Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_029133957.1 A3GO_RS0114210 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000428045.1:WP_029133957.1 Length = 449 Score = 434 bits (1117), Expect = e-126 Identities = 235/417 (56%), Positives = 295/417 (70%), Gaps = 10/417 (2%) Query: 5 LKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILATIAVCSLLMFLRVLFSTQI 64 LK + +AL+ + +LGL+ L + P L +AV S+ R+LF+ + Sbjct: 18 LKESAIAALVALGLTIVMLGLRTVDTTTGLGITTRWP--LVAVAVISVFAG-RLLFAFRR 74 Query: 65 SAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLA---LIVGALVWPF--FGSRGAVDIATL 119 WK+S G K +R+ + I ALV P F R +DIAT Sbjct: 75 E--WKASKGPVSRDRKEEEDRAATIIKRFSTIGGPVFIAFALVLPLMPFADRYVIDIATY 132 Query: 120 ILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAAT 179 +LIYVMLG GLNIVVGLAGLLDLGYV FYAVGAYSYAL + YF LSFW+CLP+AG+ AA+ Sbjct: 133 VLIYVMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALFAFYFDLSFWVCLPLAGLCAAS 192 Query: 180 FGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFER 239 FG LLGFPVLRLRGDYLAIVTLGFGEIIR+ L N T GP+GIS I +P+FFGL F+R Sbjct: 193 FGVLLGFPVLRLRGDYLAIVTLGFGEIIRIILLNWYKFTNGPDGISGIPRPSFFGLEFKR 252 Query: 240 KAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDE 299 A EG QTFH++F L+Y+S++++IFLY + L+LAL F R+ +MP+GRAWEALREDE Sbjct: 253 TAVEGTQTFHQFFDLDYSSMHRLIFLYYLILILALITNFFTLRIRKMPVGRAWEALREDE 312 Query: 300 IACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGG 359 IACR+LG+NPT KL+AF LGA FAGFAGSFFA RQ ++PESFTFIESA+ILAIVVLGG Sbjct: 313 IACRSLGINPTNTKLTAFALGAMFAGFAGSFFATRQAFISPESFTFIESAVILAIVVLGG 372 Query: 360 MGSQLGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMEL 416 MGSQ+GV +AA+++I E+ R EYRML FG LMV +M+W+P+GLL + P ++L Sbjct: 373 MGSQVGVAIAAVLLIGGTELFRGLEEYRMLAFGGLMVAIMVWKPRGLLAHREPTIKL 429 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: 618 Number of extensions: 17 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: 418 Length of database: 449 Length adjustment: 32 Effective length of query: 386 Effective length of database: 417 Effective search space: 160962 Effective search space used: 160962 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: 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