Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate PP_1018 PP_1018 mannose/glucose ABC transporter - ATP binding subunit
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Putida:PP_1018 Length = 384 Score = 327 bits (839), Expect = 2e-94 Identities = 175/366 (47%), Positives = 244/366 (66%), Gaps = 6/366 (1%) Query: 1 MTSVSVRDLSLNFGA--VTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDG 58 M ++ +R+++ +G+ L + L I GEFL+L+G SGCGKSTL+NCIAGL ++ G Sbjct: 1 MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60 Query: 59 QIFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRAS 118 I I +++V+ PKDR I MVFQSYALYP M+V +N+ FGLK+ K+P A I++ V R + Sbjct: 61 AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA 120 Query: 119 EILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKR 178 ++LQI+ LL RKP++LSGGQ+QRVA+GRAL R ++LFDEPLSNLDAKLR E+R E+K Sbjct: 121 KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 179 LHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPS 238 +HQ LK T +YVTHDQIEA+TL D++AVMK G+IQQ P IYN P N FVA FIGSP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPP 240 Query: 239 MNFFRGEVEPKDGR--SFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEA-RD 295 MNF + +DGR + + +G ++ A L+ G++++LG+RPE + + A + Sbjct: 241 MNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALE-GREIILGIRPEQIALGAADGN 299 Query: 296 GEPTHQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDA 355 G P +A V + EP G D L+++T + R+A G T+ L FD +FDA Sbjct: 300 GLPAIRAEVQVTEPTGPDLLVFVTLNQTKVCCRLAPDVACRVGDTLNLQFDPARVLLFDA 359 Query: 356 ESENRL 361 + RL Sbjct: 360 ANGERL 365 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: 395 Number of extensions: 12 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: 384 Length adjustment: 30 Effective length of query: 331 Effective length of database: 354 Effective search space: 117174 Effective search space used: 117174 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