Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate PP_0615 PP_0615 Branched-chain amino acid ABC transporter, ATP-binding protein
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__Putida:PP_0615 Length = 231 Score = 190 bits (482), Expect = 2e-53 Identities = 100/234 (42%), Positives = 155/234 (66%), Gaps = 7/234 (2%) Query: 5 ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64 +L V + Y ++G+ L+V GELVTL+G NGAGKTTTL++I G + +G I Sbjct: 1 MLNVDSIHSYYDKSHVLEGVSLKVEAGELVTLLGRNGAGKTTTLRSILGIVRPR--QGQI 58 Query: 65 EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWF 124 + GQ L G++ F++ + +A+VPE RG+F ++S++ENL + A + Q+ + + Sbjct: 59 SFNGQQLVGREIFDIARLGIALVPEHRGIFRQLSVEENLKI-AVRKTSRWQL----EDVY 113 Query: 125 AVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIR 184 ++FPRLKER LSGGEQQMLA+ARAL++ P+LL+LDEP+ GL+P++V+++ +++R Sbjct: 114 SMFPRLKERRRNGGFALSGGEQQMLAIARALLNGPRLLILDEPTEGLAPVIVDELVKILR 173 Query: 185 NVSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYL 238 + +G++ILLVEQN + A R YV+E G + QG A Q +DP +K YL Sbjct: 174 RIKDEGLSILLVEQNLMVCDALADRHYVLEQGRVAYQGSAAQFREDPSIKNRYL 227 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: 172 Number of extensions: 6 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: 241 Length of database: 231 Length adjustment: 23 Effective length of query: 218 Effective length of database: 208 Effective search space: 45344 Effective search space used: 45344 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