Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate SM_b20784 SM_b20784 branched-chain amino acid ABC transporter ATP-binding protein
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__Smeli:SM_b20784 Length = 238 Score = 137 bits (344), Expect = 2e-37 Identities = 82/237 (34%), Positives = 125/237 (52%), Gaps = 8/237 (3%) Query: 6 LKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHIE 65 L+V LS YG + ++GI V G + ++G NG GKTT L + G R EG I Sbjct: 6 LEVDNLSAGYGPTRVLEGISFSVPAGARLAVLGRNGMGKTTLLATLAGQ--TRRYEGRIR 63 Query: 66 YLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWFA 125 + S L VP+ R VF ++++ENL +G KG+ + + + Sbjct: 64 IGDANVTALPSASRALKGLGFVPQARCVFPSLTVEENLFVGL-----KGRPKTALSEAYE 118 Query: 126 VFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIRN 185 +FPRL ER + LSGGEQQML+ AR+++ P +LLLDEP GL+P++ E++ + Sbjct: 119 MFPRLYERRRNLGSQLSGGEQQMLSTARSILGRPSVLLLDEPLEGLAPVICEELMKAFAE 178 Query: 186 VS-AQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYLGEG 241 ++ G+TILLVEQ + AL+ A R ++E G + G + + + LG G Sbjct: 179 LAKTGGMTILLVEQRIQSALDFADRVIILERGRLAWSGTPEALAKEHATVERLLGVG 235 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: 141 Number of extensions: 9 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: 238 Length adjustment: 23 Effective length of query: 218 Effective length of database: 215 Effective search space: 46870 Effective search space used: 46870 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