Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Miya:8499890 Length = 350 Score = 274 bits (701), Expect = 2e-78 Identities = 159/360 (44%), Positives = 223/360 (61%), Gaps = 15/360 (4%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M+++ + ++S ++G V +D ++ +++ G LVLLG SGCGKST L IAGL V+ G+I Sbjct: 1 MSAIQLLNVSRHWGDVRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 I +R+VT P R + MVFQSYAL+P +TV +N+ FGL V K+P AE EKR+ RA +I Sbjct: 61 MIGERDVTHLPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRLTRAVDI 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 L + LL+RKP ELSGGQ+QRVA+GRALV + V L DEPLSNLDAKLR E+R EI+ L Sbjct: 121 LGLSALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMRREIRALQ 180 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 Q+L TM+YVTHDQ EA+++ADRI +M+ G I Q A P +Y+ P F FIG+P MN Sbjct: 181 QTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNFIGTPPMN 240 Query: 241 FFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTH 300 R + D R V G + + VLG+RPEH+++ +G Sbjct: 241 LVRLD----DARGSVCVAG------SRSGTVSVVDSADYVLGIRPEHIRI--VPEG---W 285 Query: 301 QAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESENR 360 +AVV+ E +G+ ++L G+ +SV + G G+ + L IFDA++ R Sbjct: 286 RAVVESVEYLGSGSVLGCRVGGEELSVVVDGVPTIAVGAEIYLHCPDEHIHIFDAKTGER 345 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: 313 Number of extensions: 13 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: 350 Length adjustment: 29 Effective length of query: 332 Effective length of database: 321 Effective search space: 106572 Effective search space used: 106572 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