Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_049754204.1 HM1_RS01340 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQH9 (318 letters) >NCBI__GCF_000019165.1:WP_049754204.1 Length = 327 Score = 271 bits (694), Expect = 1e-77 Identities = 148/305 (48%), Positives = 208/305 (68%), Gaps = 4/305 (1%) Query: 1 MKENLKV-NILWLLLLLAGYSLISVLVSVGVLNLFYVQILQQIGINIILAVGLNLIVGFS 59 MK+ L + N++ +LL Y +S + +G ++ +Y L I INIILA LN+I G + Sbjct: 1 MKKLLNLPNLIVAAVLLLFYGFVSFGLELGFIDDYYKLNLFLICINIILATSLNIINGMT 60 Query: 60 GQFSLGHAGFMAIGAYAAAIIGSKSPTYGAFFGAMLVGALLSGAVALLVGIPTLRLKGDY 119 GQFS+GHAGFMAIGAY +AI+ K F +LVGAL + LVG+PTLRLKGDY Sbjct: 61 GQFSIGHAGFMAIGAYGSAIMTMKLGY--PFPVGILVGALAAAIAGFLVGMPTLRLKGDY 118 Query: 120 LAVATLGVSEIIRIFIINGGSLTNGAAGILGIPNFTTWQMVYFFVVITTIATLNFLRSPI 179 LA+ATLG EIIR+ I+N GAAG+ GI FT+W+ ++F V T + NF+ S Sbjct: 119 LAIATLGFGEIIRVIILNI-EYVGGAAGLNGISQFTSWEWLFFLTVATVLIIKNFMTSTH 177 Query: 180 GRSTLSVREDEIAAESVGVNTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINS 239 GR+ +++RE+EIAAE++G++ T+ K+IAF GA A IAGSL A + ++ P + F+ S Sbjct: 178 GRACIAIRENEIAAETMGIDITRYKVIAFTMGAFFAGIAGSLHAHYFYTIQPTTFGFMKS 237 Query: 240 INVLIIVVFGGLGSITGAIVSAIVLGILNMLLQDVASVRMIIYALALVLVMIFRPGGLLG 299 ++L+ VV GGLGS+TG+++SAI L IL+ LQ+ A +RM+IY+L LV+VM+ RP GL+G Sbjct: 238 FDILVFVVLGGLGSLTGSVISAIALTILSAFLQEYAELRMVIYSLLLVIVMLVRPQGLMG 297 Query: 300 TWELS 304 T E S Sbjct: 298 TAEFS 302 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: 279 Number of extensions: 14 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: 318 Length of database: 327 Length adjustment: 28 Effective length of query: 290 Effective length of database: 299 Effective search space: 86710 Effective search space used: 86710 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: 48 (23.1 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