Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate Ac3H11_1610 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1610 Length = 362 Score = 225 bits (573), Expect = 2e-63 Identities = 124/308 (40%), Positives = 190/308 (61%), Gaps = 13/308 (4%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M+ + + D++ +G+ + +NL ++ GEF+ LLG SGCGK+T L +AG V+ G+I Sbjct: 1 MSFLQLTDVTKFYGSTCAVQSMNLSVEKGEFVSLLGPSGCGKTTTLQMVAGFEAVTSGRI 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 + R++T + RG+G+VFQSYAL+P MTV N+SFGL++ K+P AE + RV +A + Sbjct: 61 ELAGRDITHAKANTRGLGIVFQSYALFPHMTVADNVSFGLEMRKVPKAERKDRVAQALGL 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 + ++ R P ELSGGQRQRVA+ RALV + V L DEPLSNLDAKLR E++ E++++ Sbjct: 121 VHLEKHAGRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDAKLREEMQFELRQIQ 180 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 + + T + VTHDQ EA++++DR+ VM++G Q+ P +Y P F++ F+G N Sbjct: 181 RKVGTTTVMVTHDQSEAMSISDRVVVMEAGRATQIDHPHRVYEHPRTRFISTFVG--KAN 238 Query: 241 FFRGEVEPKDG-RSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPT 299 G+V + V AG I V + +PG V+L +RPE +++ PT Sbjct: 239 LVPGQVTTASATHTHVGAGPIEVRVEG----AQFRPGAAVLLSVRPEKLQL------VPT 288 Query: 300 HQAVVDIE 307 Q +D E Sbjct: 289 VQGRIDGE 296 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: 335 Number of extensions: 14 Number of successful extensions: 2 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: 362 Length adjustment: 29 Effective length of query: 332 Effective length of database: 333 Effective search space: 110556 Effective search space used: 110556 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