Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate GFF2761 HP15_2705 inner-membrane translocator
Query= uniprot:A0A159ZYE0 (418 letters) >FitnessBrowser__Marino:GFF2761 Length = 335 Score = 186 bits (473), Expect = 7e-52 Identities = 110/317 (34%), Positives = 176/317 (55%), Gaps = 15/317 (4%) Query: 94 IVLALIVGALVWPFFGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAY 153 ++LALI+ ++ F G+ ++ T + I +GLN++VG AG + LG+ GF+ +GAY Sbjct: 14 VILALIL-VILPAFLGNPFHYELVTQMAIIAATVVGLNLLVGFAGQISLGHAGFFGLGAY 72 Query: 154 SYALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRN 213 + + +G S L + ++ +++G P+LRL+G YL++ TL G II + L N Sbjct: 73 FTGIATGTYGWSSVPALVVGAIVVGAIAWIVGRPILRLKGHYLSMATLAVGFIIAIILNN 132 Query: 214 LTDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEY--FGLEYNSINKVIFLYLVALL 271 +TGGP+G+ P F +E L F Y FG+ Y+ A + Sbjct: 133 ERALTGGPDGMP---VPAFEIFGWE------LSAFGRYSLFGITIEGFQA---WYIFASV 180 Query: 272 LALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFF 331 + L A++ L+ PIGRA ++ E+A +G+N K F + A +A GS + Sbjct: 181 VLLVAVWFALNLIESPIGRALRSVHGSEVAASVVGVNTAKYKSLVFVISAIYASLMGSLY 240 Query: 332 AARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMREFSEYRMLMF 391 A QG +TP +F S + + +VVLGGMGS GVIL A+V+ LLP+++ +F E +MF Sbjct: 241 AHFQGFITPAVASFEFSILFITMVVLGGMGSTFGVILGAVVLKLLPQVLADFQELEHVMF 300 Query: 392 GALMVLMMIWRPQGLLP 408 G +++L MI+ P+GLLP Sbjct: 301 GLILMLTMIFMPKGLLP 317 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: 479 Number of extensions: 29 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: 1 Length of query: 418 Length of database: 335 Length adjustment: 30 Effective length of query: 388 Effective length of database: 305 Effective search space: 118340 Effective search space used: 118340 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 17 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