Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Marino:GFF3011 Length = 372 Score = 329 bits (844), Expect = 6e-95 Identities = 174/369 (47%), Positives = 244/369 (66%), Gaps = 8/369 (2%) Query: 1 MTSVSVRDLSLNFGAVT--VLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDG 58 M+ + +R + + V L +++DI GEFL+L+G SGCGKSTL+N IAGL ++DG Sbjct: 1 MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60 Query: 59 QIFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRAS 118 I + ++++ EPKDR I MVFQSYALYP M+V +N++FGLK+ +P EI++ V+R + Sbjct: 61 SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120 Query: 119 EILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKR 178 ++LQI PL+ +KP+ LSGGQ+QRVA+GRAL R ++LFDEPLSNLDAKLR E+R EIK+ Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180 Query: 179 LHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPS 238 LHQ LK T++YVTHDQIEA+TLADRIAV+K G +QQL P +Y+ PENLFVAGF+GSP+ Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240 Query: 239 MNFFRGEVEPKDG--RSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDG 296 M+F VE +G ++ VR P + G+KV+LG+RPEH+ + + Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGKKVILGIRPEHITQPQDQKN 300 Query: 297 EPTHQA----VVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASI 352 + T A +++ EP G D + + ++ RI + G T L FDM Sbjct: 301 DQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELMFDMKKVVF 360 Query: 353 FDAESENRL 361 FD E+E R+ Sbjct: 361 FDPETEKRI 369 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: 447 Number of extensions: 18 Number of successful extensions: 3 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: 372 Length adjustment: 30 Effective length of query: 331 Effective length of database: 342 Effective search space: 113202 Effective search space used: 113202 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