Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate PP_0411 PP_0411 Polyamine ABC transporter, ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Putida:PP_0411 Length = 374 Score = 224 bits (572), Expect = 2e-63 Identities = 132/298 (44%), Positives = 180/298 (60%), Gaps = 18/298 (6%) Query: 2 TSVSVRDLSLNF-GAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 T VS R + ++ G ++ LNLDI GEFL LLG SG GK+T L +AG + G+I Sbjct: 13 TLVSFRGVQKSYDGESLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEI 72 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 + R++ P R IGMVFQ+YAL+P MTV +NL+F L V + +I +RVKR + Sbjct: 73 QLGGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRNLSKTDISERVKRVLNM 132 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 +Q+ KR P +LSGGQ+QRVA+ RALV + + L DEPL LD +LR +++EIK +H Sbjct: 133 VQLDAFAKRYPGQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHIH 192 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 Q L T++YVTHDQ EALT++DR+AV G IQQ+ADP T+Y P N FVA FIG N Sbjct: 193 QRLGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIADPRTLYEEPCNTFVANFIG--ENN 250 Query: 241 FFRGEVEPKDGRSF-------VRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVD 291 G + DG+ R +A +V Q G+ V L +RPE V+++ Sbjct: 251 RISGTLLASDGKRCQVQLPRGERVEALAVNVG--------QAGEPVTLSIRPERVRLN 300 Lambda K H 0.320 0.137 0.392 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: 389 Number of extensions: 15 Number of successful extensions: 1 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: 361 Length of database: 374 Length adjustment: 30 Effective length of query: 331 Effective length of database: 344 Effective search space: 113864 Effective search space used: 113864 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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