Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate HSERO_RS08920 HSERO_RS08920 ABC transporter
Query= TCDB::Q8DQH9 (318 letters) >FitnessBrowser__HerbieS:HSERO_RS08920 Length = 655 Score = 146 bits (368), Expect = 2e-39 Identities = 98/290 (33%), Positives = 158/290 (54%), Gaps = 16/290 (5%) Query: 12 LLLLLAGYSLISVLVSVGVLNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMA 71 LLL L G ++ + V V N +Y+ +++ I I IL GL+++VG++GQ SLGHAG Sbjct: 6 LLLSLLGIVALAGIPMV-VHNPYYLHLIETILIYAILLFGLDIVVGYTGQVSLGHAGLFG 64 Query: 72 IGAYAAAIIGSK--SPTYGAFFGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSE 129 IG+YAA ++ K P + A+ V A+ +AL P LR+ G YLA+ TL Sbjct: 65 IGSYAAGVLFFKLGMPIFVTVPAAIAVTAVFGAILAL----PALRVTGPYLAMVTLAFGT 120 Query: 130 IIRIFIINGGSLTNGAAGI------LGIPNFTTWQMVYFFVVITTIATL---NFLRSPIG 180 II+I I LT G GI +G + Q Y V+ ++ L L+S +G Sbjct: 121 IIQILINEMTFLTEGPLGIKLQKPMIGGDKMSEVQFFYLVAVLMVLSMLVVHRILKSNLG 180 Query: 181 RSTLSVREDEIAAESVGVNTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINSI 240 R+ ++R+ IA++ +GV+ + K+ AF+ A A ++G+L A + P Y F +I Sbjct: 181 RAFQALRDSPIASDCMGVSVYRYKVYAFIISAALAGLSGALYAYSEEYISPNTYNFELTI 240 Query: 241 NVLIIVVFGGLGSITGAIVSAIVLGILNMLLQDVASVRMIIYALALVLVM 290 L+ V+ GG S G+++ A+++ +L LL D+A R I LA+++V+ Sbjct: 241 MFLLAVIMGGRKSRIGSLIGALIVVMLPSLLSDIALFRQIATVLAVIVVV 290 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: 348 Number of extensions: 16 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: 655 Length adjustment: 33 Effective length of query: 285 Effective length of database: 622 Effective search space: 177270 Effective search space used: 177270 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: 51 (24.3 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