Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate GFF3203 PGA1_c32560 high-affinity branched-chain amino acid transport ATP-binding protein
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__Phaeo:GFF3203 Length = 278 Score = 215 bits (547), Expect = 8e-61 Identities = 114/241 (47%), Positives = 162/241 (67%), Gaps = 6/241 (2%) Query: 5 ILKVQQLSVAYGGIQAV-KGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVE-- 61 +L+V + V Y + V KG+ L+V +G + L+G NGAGKTTTLKA++ L + R E Sbjct: 15 LLEVNNIEVIYNHVILVLKGVSLKVPKGGITALLGGNGAGKTTTLKAVSNLLHSERGEVT 74 Query: 62 -GHIEYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYT-SDDKGQIAAD 119 G I Y G+ ++ + ELVK + V EGR F ++++ENLL GAYT SD I D Sbjct: 75 KGSISYRGERIQDRDPAELVKKGVIQVMEGRHCFEHLTVEENLLTGAYTRSDGNANIQRD 134 Query: 120 IDKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKI 179 ++ ++ FPRLKER AG SGGEQQM+AM RALMS P+ +LLDEPSMGL+P +VE+I Sbjct: 135 LEMVYSYFPRLKERRRSQAGYTSGGEQQMVAMGRALMSRPETILLDEPSMGLAPQLVEQI 194 Query: 180 FEVIRNVSA-QGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYL 238 FE++++++ +G+T LL EQN +AL +H GY++ESG + M G A ++ ++P VK YL Sbjct: 195 FEIVKSINENEGVTFLLAEQNTNVALRYSHYGYILESGRVVMDGPAAELRENPDVKEFYL 254 Query: 239 G 239 G Sbjct: 255 G 255 Lambda K H 0.317 0.134 0.365 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: 205 Number of extensions: 11 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: 241 Length of database: 278 Length adjustment: 24 Effective length of query: 217 Effective length of database: 254 Effective search space: 55118 Effective search space used: 55118 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 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