Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_008509836.1 BIBO1_RS16200 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_000182725.1:WP_008509836.1 Length = 333 Score = 276 bits (706), Expect = 6e-79 Identities = 159/350 (45%), Positives = 217/350 (62%), Gaps = 39/350 (11%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M + +RD+ +FG+ V+ +++DI GEF+V +G SGCGKSTLL IAGL +++ G + Sbjct: 1 MAELQLRDVRKSFGSFEVIKGVDMDIRPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 I V P RGI MVFQSYALYP MTV +N++FG+++A E + R+ A+E+ Sbjct: 61 SINGAVVNNFNPSRRGIAMVFQSYALYPHMTVYENMAFGMQLASKSRQECKARIHAAAEM 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 LQ+ P L+R P +LSGGQRQRVAIGRA+VRD VFLFDEPLSNLDA LR R+EI RLH Sbjct: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIARLH 180 Query: 181 QSLKN-TMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSM 239 QS+++ TMIYVTHDQ+EA+TLADRI V++ G ++Q+ P+ +Y P +LFVAGFIGSP M Sbjct: 181 QSMEDTTMIYVTHDQVEAMTLADRICVLRDGRVEQIGTPLELYEKPNSLFVAGFIGSPKM 240 Query: 240 NFFRG-EVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEAR---D 295 NF G EP + AHT +GLR EH+ + R Sbjct: 241 NFLTGPHAEP------------------FGAHT---------VGLRSEHLAIVPERGHWS 273 Query: 296 GEPTHQAVVDIEEPMGADNLLWLTFA-GQSMSVRIAGQRRYPPGSTVRLS 344 G+ H E +G+D +++ + + VR +G PG + +S Sbjct: 274 GQVVH------TEILGSDTYVYIDLGLEEPLVVRESGVSARKPGEALSIS 317 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: 344 Number of extensions: 16 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: 333 Length adjustment: 29 Effective length of query: 332 Effective length of database: 304 Effective search space: 100928 Effective search space used: 100928 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 24 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