Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate Dsui_1113 Dsui_1113 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__PS:Dsui_1113 Length = 278 Score = 196 bits (497), Expect = 5e-55 Identities = 107/242 (44%), Positives = 158/242 (65%), Gaps = 6/242 (2%) Query: 4 NILKVQQLSVAYGGIQAV-KGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASR--- 59 N L + + V Y + V KG+ L V +G++V L+GANGAGK+TTLKAI+ L A R Sbjct: 14 NYLSINNIEVIYDHVILVLKGVSLTVPKGKIVALLGANGAGKSTTLKAISNLLHAERGDV 73 Query: 60 VEGHIEYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYT-SDDKGQIAA 118 +G +E+ G + ELVK + V EGR F +SI+ENLL GAYT + + ++ Sbjct: 74 TKGSVEFKGTRVDQLTPNELVKRGVIQVMEGRHCFAHLSIEENLLTGAYTRGNSRAELKQ 133 Query: 119 DIDKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEK 178 +++ + FPRLK R AG SGGEQQM A+ RALM+ P+++LLDEPSMGL+P +VE+ Sbjct: 134 NLEMVYHYFPRLKTRRTSQAGYTSGGEQQMCAIGRALMAKPEMILLDEPSMGLAPQIVEE 193 Query: 179 IFEVIRNV-SAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAY 237 IFE+++++ S + ++ LL EQN +AL A GY++E+G + M+G A+++ + VK Y Sbjct: 194 IFEIVKDLNSRENVSFLLAEQNTMVALRYADLGYILENGRVVMEGDAKELASNEDVKEFY 253 Query: 238 LG 239 LG Sbjct: 254 LG 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: 172 Number of extensions: 13 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