Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Keio:14400 Length = 348 Score = 217 bits (553), Expect = 3e-61 Identities = 129/340 (37%), Positives = 195/340 (57%), Gaps = 27/340 (7%) Query: 4 VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIK 63 V +R+++ FG+ TV+D +NL I G+ + LLG SGCGK+T+L +AGL S+GQIFI Sbjct: 7 VELRNVTKRFGSNTVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIFID 66 Query: 64 DRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQI 123 +VT + R I MVFQSYAL+P M++ +N+ +GLK+ +P AE++ RVK A ++ + Sbjct: 67 GEDVTHRSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEALAMVDL 126 Query: 124 QPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSL 183 + R ++SGGQ+QRVA+ RAL+ V LFDEPLSNLDA LR +R +I+ L + Sbjct: 127 EGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIRELQKQF 186 Query: 184 KNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSM---N 240 T +YVTHDQ EA ++D + VM G I Q+ P +Y P + F+A F+G ++ Sbjct: 187 DITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFMGDANLFPAT 246 Query: 241 FFRGEVEPKDGRSFVRAGGIAFDVTAY----PAHTRLQPGQKVVLGLRPEHVKVDEARDG 296 F G V D+ Y P H Q G+ +V G+RPE + + + G Sbjct: 247 FSDGYV----------------DIYGYHLPRPLHFGTQ-GEGMV-GVRPEAITLSDR--G 286 Query: 297 EPTHQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYP 336 E + + V+ MG + + + GQ + +++ R P Sbjct: 287 EESQRCVIRHVAYMGPQYEVTVEWHGQEILLQVNATRLQP 326 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: 322 Number of extensions: 13 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: 348 Length adjustment: 29 Effective length of query: 332 Effective length of database: 319 Effective search space: 105908 Effective search space used: 105908 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