Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_085770499.1 B1812_RS04360 ABC transporter ATP-binding protein
Query= uniprot:D8IUY7 (241 letters) >NCBI__GCF_002117405.1:WP_085770499.1 Length = 266 Score = 191 bits (485), Expect = 1e-53 Identities = 103/244 (42%), Positives = 161/244 (65%), Gaps = 6/244 (2%) Query: 2 TTNILKVQQLSVAYG-GIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASR- 59 T +L+++ + +Y I A++ + L+V GE+V L+GANG+GKTT L A + L A R Sbjct: 4 TETLLELRDVEASYNQAIVALRDVSLKVRRGEIVALLGANGSGKTTILNATSRLLAAERG 63 Query: 60 --VEGHIEYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTS-DDKGQI 116 G I + G+ + EL + L V EGR VF ++++ENL GA ++ ++ Sbjct: 64 QITSGKILFDGRSTSKSSTAELAQKGLVQVLEGRRVFRSLTVEENLASGALARRSNRREL 123 Query: 117 AADIDKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMV 176 D+D + VFP+LK R +AG LSGGEQQM A+ RA+M+HP+LL+LDEPSMGL+P++V Sbjct: 124 RDDLDYVYGVFPQLKHRRRSLAGLLSGGEQQMTAIGRAMMTHPRLLILDEPSMGLAPLVV 183 Query: 177 EKIFEVIRNVS-AQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKA 235 E+I++V+ ++ +G+++L+ EQNA +AL AHRGYV+E+G++ ++G A + + VK Sbjct: 184 EEIYQVLGALNRMKGLSLLVAEQNAYVALRHAHRGYVVENGVVVLEGAAATLQEREDVKD 243 Query: 236 AYLG 239 YLG Sbjct: 244 FYLG 247 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: 150 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: 266 Length adjustment: 24 Effective length of query: 217 Effective length of database: 242 Effective search space: 52514 Effective search space used: 52514 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