Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate BPHYT_RS05040 BPHYT_RS05040 sugar ABC transporter ATPase
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__BFirm:BPHYT_RS05040 Length = 371 Score = 331 bits (849), Expect = 2e-95 Identities = 187/370 (50%), Positives = 237/370 (64%), Gaps = 9/370 (2%) Query: 1 MTSVSVRDLSLNF-GAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQ 59 M S+S+RD+ + V VL +N+DI+ G+FL+L+G SGCGKSTLLN IAGL V+ G+ Sbjct: 1 MASLSIRDVYKTYPNGVPVLKGVNIDIEDGQFLILVGGSGCGKSTLLNMIAGLETVTKGE 60 Query: 60 IFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASE 119 I I + V PKDR I MVFQSYALYP MTV +N+SFGL + K+P E + V R S Sbjct: 61 IQIDGKTVNNLSPKDRDIAMVFQSYALYPSMTVRENISFGLNIRKVPKNEQTQIVDRVSN 120 Query: 120 ILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRL 179 LQI LL RKP +LSGGQRQRVA+GRAL RD +FLFDEPLSNLDAKLR E+R EIK L Sbjct: 121 TLQITHLLDRKPGQLSGGQRQRVAMGRALARDPVMFLFDEPLSNLDAKLRIEMRSEIKLL 180 Query: 180 HQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSM 239 HQ L T++YVTHDQIEA+TL DRIAVMK G++QQ P IY++P NLFVAGFIG+P M Sbjct: 181 HQRLGTTIVYVTHDQIEAMTLGDRIAVMKDGIVQQFGAPQEIYDSPSNLFVAGFIGAPPM 240 Query: 240 NFFRGE-VEPKDGRSFVRAGGIAFDVTAYP---AHTRLQPGQKVVLGLRPEHVKVDEARD 295 NF +G+ VE G + G+A P A R G++V+LGLRPE + Sbjct: 241 NFIQGKLVEQGAGVALELDTGVARTALNLPFDSAKVRSHVGREVILGLRPERITDARGAH 300 Query: 296 GEPTH----QAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVAS 351 G+ + VD+ EP G D L++ G+ + R+ P + L FD A Sbjct: 301 GDNAKLQPIEVKVDVIEPTGPDTLVFAQVNGKRIVSRVHPASNPQPLANTTLLFDTSKAV 360 Query: 352 IFDAESENRL 361 +FD +E R+ Sbjct: 361 LFDPSNEERI 370 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: 432 Number of extensions: 19 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: 371 Length adjustment: 30 Effective length of query: 331 Effective length of database: 341 Effective search space: 112871 Effective search space used: 112871 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