Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__SynE:Synpcc7942_0947 Length = 355 Score = 252 bits (643), Expect = 1e-71 Identities = 143/333 (42%), Positives = 202/333 (60%), Gaps = 11/333 (3%) Query: 15 AVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEEPKD 74 +V + L+L + GEFL LLG SGCGKST L IAGL + G I++ DR +T P D Sbjct: 18 SVVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIWLGDREITTLPPGD 77 Query: 75 RGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKRKPSEL 134 R + MVFQSYALYP + V +NL+ GL++ + AEIE+R+++ + L++ LL R+P++L Sbjct: 78 RDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNLELDHLLDRRPAQL 137 Query: 135 SGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMIYVTHDQ 194 SGGQRQRVA+GRALVR VFL DEPLSNLDA LR ++R ++K L + ++YVTHDQ Sbjct: 138 SGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFSQQASPVVYVTHDQ 197 Query: 195 IEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVEPKDGRSF 254 EAL+L+ RIA++ G +QQL P IY AP N FVAGFIGSP MN Sbjct: 198 TEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNLLPLP--------- 248 Query: 255 VRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTHQAVVDIEEPMGADN 314 + +G A P + L +V+ GLRPEH+K+ + E + + E +G Sbjct: 249 IHSGQAWLGSRALPIPSHLAARSQVLWGLRPEHLKL-ATPEVERAIPVQLHLTENLGMQR 307 Query: 315 LLWLTFAGQ-SMSVRIAGQRRYPPGSTVRLSFD 346 LL + A + +R+ P + ++++F+ Sbjct: 308 LLTVAIAANPEVRLRLLMPSDQPIPTDLQVTFE 340 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: 337 Number of extensions: 10 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: 355 Length adjustment: 29 Effective length of query: 332 Effective length of database: 326 Effective search space: 108232 Effective search space used: 108232 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