Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_012171467.1 AZC_RS15210 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000010525.1:WP_012171467.1 Length = 480 Score = 336 bits (862), Expect = 8e-97 Identities = 203/438 (46%), Positives = 267/438 (60%), Gaps = 39/438 (8%) Query: 5 LKSALFSALLVWAVAYPVLGLKLTIVG---INLEVHGTSPAILAT-IAVCSLLMFLRVLF 60 LK A+ S +L + + P++G + T G + L I A +A L++ L + Sbjct: 22 LKDAVVSGVLTFLLLLPLVGFRATESGSGPLTLTYRFGLVTIFALLVAGLRLVLNLTLWR 81 Query: 61 STQISAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLI 120 ++ A L V+ + + F I+ L+ L SR +D+ I Sbjct: 82 EGRVKATKSGPSALAVVGNQMAPFAKSAFFAIAILYPLLAVLLSGGLTPSRYWIDLGIYI 141 Query: 121 LIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLS---------------HYFGL- 164 YVMLG GLNIVVGLAGLLDLGYV FYAVGAY++ALLS +++ L Sbjct: 142 GSYVMLGWGLNIVVGLAGLLDLGYVAFYAVGAYAFALLSTSVPINDWMAGHLGENFWALW 201 Query: 165 SFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGI 224 SFW+CLP+ G++AA +G +LGFPVLRLRGDYLAIVTL FGEIIRL L N TD T G GI Sbjct: 202 SFWVCLPVCGLLAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDFTNGAAGI 261 Query: 225 SNIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLL 284 ++I +FFG+ F + G F FGL ++ ++++IFLY V + L+ RL Sbjct: 262 ASIPPISFFGIPF----SSGDDGFAALFGLTFDPMHRIIFLYFVIVALSALTALATLRLR 317 Query: 285 RMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFT 344 RMP+GRAWEALREDEIACR+LG+N T+ KL+AF GA F GFAG+FFA R V+PESFT Sbjct: 318 RMPVGRAWEALREDEIACRSLGINTTLTKLTAFATGAMFGGFAGAFFAVRVRFVSPESFT 377 Query: 345 FIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMREF---------------SEYRML 389 F+ESA+ILAIVVLGGMGSQ+GV AA+ MI EM+R + YRML Sbjct: 378 FMESAMILAIVVLGGMGSQMGVAAAAVFMIGGMEMLRNLTFLKSDWLLGPDFDPTLYRML 437 Query: 390 MFGALMVLMMIWRPQGLL 407 +FG MV +M+WRP+G++ Sbjct: 438 IFGFAMVAVMVWRPRGIV 455 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: 660 Number of extensions: 41 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: 480 Length adjustment: 33 Effective length of query: 385 Effective length of database: 447 Effective search space: 172095 Effective search space used: 172095 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