Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_015928428.1 MNOD_RS08410 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000022085.1:WP_015928428.1 Length = 474 Score = 375 bits (962), Expect = e-108 Identities = 222/442 (50%), Positives = 282/442 (63%), Gaps = 35/442 (7%) Query: 5 LKSALFSALLVWAVAYPVLGLKLTIVG----INLEVHGTSPAILATIAVCSLLMFLRVLF 60 +K A AL+ + + P++ + + G ++L AIL + + L VL Sbjct: 26 VKDAALFALVTFGLCVPIVSYRTDLGGEGGALSLTPRWGLVAILCGLVFAARLAQRIVLA 85 Query: 61 STQISAMWKSSP-----GLPVIPAKASNF--LTLPTTQRWIVLALIVGALVWPFFG---- 109 + + SP + P A L LP ++ +AL LV G Sbjct: 86 NRDVRRALTPSPRQATEAVDATPNAAQKISGLALPV---FLGVALAFPLLVVLGTGGLSE 142 Query: 110 SRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWIC 169 SR VD+ LIL YVMLG GLNIVVGLAGLLDLGYV FYAVGAY+YALLS F LSFWIC Sbjct: 143 SRYWVDLGILILTYVMLGWGLNIVVGLAGLLDLGYVAFYAVGAYTYALLSTTFDLSFWIC 202 Query: 170 LPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEK 229 LP+AG+ AA +G +LGFPVLRLRGDYLAIVTL FGEIIRL L N +D++GG G+S+I + Sbjct: 203 LPLAGLFAACWGMILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWSDLSGGAAGVSSIPR 262 Query: 230 PTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIG 289 TFFG+ F F FG+ ++ +++V+FLY + L LAL V RL R+P+G Sbjct: 263 VTFFGVPFTADE----DGFAARFGITFDPMHRVVFLYYLILTLALVTNLVTLRLRRLPLG 318 Query: 290 RAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESA 349 RAWEALREDEIACR+LG+N T KL+AF LGA F G AGSFFA RQG V+PESF F+ESA Sbjct: 319 RAWEALREDEIACRSLGINTTNTKLTAFALGAMFGGIAGSFFAVRQGFVSPESFNFLESA 378 Query: 350 IILAIVVLGGMGSQLGVILAAIVMILLPEMMREF-------------SEYRMLMFGALMV 396 IILAIVVLGGMGSQ+GV +AA+ M+ PE++R SEYR+L+FG MV Sbjct: 379 IILAIVVLGGMGSQIGVAIAAVAMVGGPELLRNLGFLRAVFGEGFDPSEYRLLLFGLAMV 438 Query: 397 LMMIWRPQGLLPMQRPHMELRK 418 LMMIWRP+GL+ + P + L++ Sbjct: 439 LMMIWRPRGLISERAPSVVLKE 460 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: 663 Number of extensions: 37 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: 474 Length adjustment: 32 Effective length of query: 386 Effective length of database: 442 Effective search space: 170612 Effective search space used: 170612 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