Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate PP_2753 PP_2753 putative Branched-chain amino acid ABC transporter, ATP-binding protein
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__Putida:PP_2753 Length = 257 Score = 196 bits (499), Expect = 3e-55 Identities = 106/245 (43%), Positives = 161/245 (65%), Gaps = 6/245 (2%) Query: 1 MTTNILKVQQLSVAYGG-IQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASR 59 +++ +L V+ + V Y G I AV G+ L V +G++V L+GANGAGK+TTLKAI+G + A R Sbjct: 10 VSSELLAVEDIEVIYDGTILAVAGVSLRVGQGDIVALLGANGAGKSTTLKAISGLVQADR 69 Query: 60 VE---GHIEYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDD-KGQ 115 GHI + GQ G + L + + V EGR VF+ ++I+ENL G + + + Q Sbjct: 70 AHVSRGHIRFQGQDTAGVAANLLARQGIVHVLEGRHVFSHLTIEENLRSGGFLRNPTRRQ 129 Query: 116 IAADIDKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIM 175 + D+++ +A FPRLK + AG SGGEQQMLA+ RALM+ P+L+LLDEPSMGL+PI+ Sbjct: 130 LEQDLERIYAWFPRLKTKRKTQAGLTSGGEQQMLAIGRALMTKPRLVLLDEPSMGLAPII 189 Query: 176 VEKIFEVIRNVSA-QGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVK 234 VE+IF ++ ++A QG++ L+ EQN +AL A Y++E+G + +G A ++ ++ Sbjct: 190 VEEIFAIVAQLNAQQGVSFLVAEQNINVALRYASHAYILENGRVVGEGSAAELAAREDIQ 249 Query: 235 AAYLG 239 YLG Sbjct: 250 HFYLG 254 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: 167 Number of extensions: 8 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: 257 Length adjustment: 24 Effective length of query: 217 Effective length of database: 233 Effective search space: 50561 Effective search space used: 50561 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: 46 (22.3 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