Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate GFF4157 HP15_4097 inner-membrane translocator
Query= TCDB::Q8DQH9 (318 letters) >FitnessBrowser__Marino:GFF4157 Length = 347 Score = 157 bits (397), Expect = 4e-43 Identities = 103/326 (31%), Positives = 171/326 (52%), Gaps = 33/326 (10%) Query: 10 LWLLLLLAGYSLISVLVSVGVLNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGF 69 LWL G+ L+ +LV V++ + + + +GI +I GLN++ GF+G SLG AGF Sbjct: 24 LWL-----GFFLLILLVFPFVVDSYLLYLGCLVGIAVISTTGLNILTGFTGLISLGQAGF 78 Query: 70 MAIGAYAAAIIGSKSPTYGAFFGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSE 129 M +GAY A + + F +++ L++ AV +LVG+P+LR+KG YLA+ATL S Sbjct: 79 MGVGAYTVAWLSINTAL--PFPVTLVLAGLMAAAVGILVGLPSLRVKGLYLAIATLAASV 136 Query: 130 IIRIFIINGGSLTNGAAGILGIP------NFTTWQMVYFFVV----ITTIATLNFLRSPI 179 + S+T G G+ P F + M+YF +V + +A N R+ I Sbjct: 137 FLHFIFAEWESVTGGMGGLSLEPAHLFGLTFQSDFMMYFIIVPLAVLMVLAARNVFRTRI 196 Query: 180 GRSTLSVREDEIAAESVGVNTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINS 239 GR+ +++R+ +I+AE +G+N + K+++F + A IAG L A F V P+ + S Sbjct: 197 GRAFIAIRDRDISAEILGINLLRYKLMSFALSSFYAGIAGGLFAYFYRVVTPESFPLSMS 256 Query: 240 INVLIIVVFGGLGSITGAIVSAIVLGILNMLLQ---------------DVASVRMIIYAL 284 I L V+ GG+G++ G I+ A + ++ L+ ++ + II+ Sbjct: 257 IFYLAAVIVGGMGNLLGGILGAAFMTLVPEALKLLTAALTPFYPNAPVFMSPMLEIIFGA 316 Query: 285 ALVLVMIFRPGGLLGTWELSLSRFFK 310 +V +IF P GL W + RFF+ Sbjct: 317 LIVGFLIFEPHGLAEIWH-RIRRFFR 341 Lambda K H 0.327 0.143 0.403 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: 241 Number of extensions: 18 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: 318 Length of database: 347 Length adjustment: 28 Effective length of query: 290 Effective length of database: 319 Effective search space: 92510 Effective search space used: 92510 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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