Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein
Query= uniprot:D8IUY7 (241 letters) >NCBI__GCF_000016765.1:WP_041378948.1 Length = 252 Score = 90.9 bits (224), Expect = 2e-23 Identities = 71/230 (30%), Positives = 112/230 (48%), Gaps = 16/230 (6%) Query: 15 YGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHIEYLGQPLKGK 74 Y G + + L + G V L+GA+GAGKTT LKAI + G I G+ + + Sbjct: 11 YAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEID--TGTIAIEGRDVAAQ 68 Query: 75 KSFELVKDKLAMVPEGRGVFTRMSIQENL-----LMGAYTSDDKGQIAADIDKWFAVFPR 129 EL + ++ V +G G+F MS+ EN+ L G + ++A +D Sbjct: 69 PVAEL-RRRIGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLDLVALPADF 127 Query: 130 LKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIRNV-SA 188 + R AQ LSGG+ Q + ARAL + P ++L+DEP L P+ +++ R + A Sbjct: 128 AERRPAQ----LSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALHEA 183 Query: 189 QGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQML---DDPRVKA 235 G+T L+V + AL A R V+ G I + ++ DPR++A Sbjct: 184 MGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPRALIHGAGDPRIEA 233 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: 155 Number of extensions: 8 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: 252 Length adjustment: 24 Effective length of query: 217 Effective length of database: 228 Effective search space: 49476 Effective search space used: 49476 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 Apr 09 2024. 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