Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_042441258.1 TX73_RS20505 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000195775.1:WP_042441258.1 Length = 314 Score = 185 bits (470), Expect = 1e-51 Identities = 107/317 (33%), Positives = 178/317 (56%), Gaps = 24/317 (7%) Query: 94 IVLALIVGALVWPF-FGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGA 152 I++AL V V P F S +A+L+ + + +GLNI++G AG + LG+ GF+ +GA Sbjct: 11 ILIALAVVMAVLPLLFPSSYYFRVASLVWVSALAAIGLNILMGKAGQVSLGHAGFFGIGA 70 Query: 153 YSYALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLR 212 Y+ A+ + GL+ + + + +++A FL+G P+LRL+G YLAI TLG G ++ + + Sbjct: 71 YAVAIGPAHLGLNALLAVLVGALLSALLAFLVGRPILRLKGHYLAIATLGLGVLVAMVIT 130 Query: 213 NLTDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLL 272 + TGGP+G+ + K + FG G T++ ++ A LL Sbjct: 131 TESGWTGGPDGMP-VPKLSLFGWRIS-----GSNTWY----------------WITAGLL 168 Query: 273 ALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFA 332 + F +N L P GRA+ AL + EIA R G++ KL AF + A +A AGS A Sbjct: 169 LIGTWFALN-LDDTPTGRAFRALHDSEIAARTAGVHVERFKLQAFVIAAVYASIAGSALA 227 Query: 333 ARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMREFSEYRMLMFG 392 G V P+ F+ S ++ +VVLGG+GS +G I+ A V+++LP+++ F +Y + G Sbjct: 228 MMNGFVNPDQAGFLHSVELVTMVVLGGLGSIVGSIVGAAVLVVLPQLLTVFQDYEHFLLG 287 Query: 393 ALMVLMMIWRPQGLLPM 409 ++++ MI+ G++PM Sbjct: 288 LIIIVSMIFMRDGMVPM 304 Score = 23.5 bits (49), Expect = 0.009 Identities = 12/22 (54%), Positives = 14/22 (63%) Query: 5 LKSALFSALLVWAVAYPVLGLK 26 L AL SALL + V P+L LK Sbjct: 89 LVGALLSALLAFLVGRPILRLK 110 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: 374 Number of extensions: 25 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: 418 Length of database: 314 Length adjustment: 29 Effective length of query: 389 Effective length of database: 285 Effective search space: 110865 Effective search space used: 110865 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: 49 (23.5 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