Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate H281DRAFT_03749 H281DRAFT_03749 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Burk376:H281DRAFT_03749 Length = 360 Score = 298 bits (762), Expect = 2e-85 Identities = 165/364 (45%), Positives = 225/364 (61%), Gaps = 8/364 (2%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M +V + + +G V+ ++L ID GEF+VL+G SGCGKSTL+ +AGL ++S G + Sbjct: 1 MAAVQLSGIFKRYGDTQVVHGIDLHIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDL 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 I P+ R I MVFQSYALYP ++V +N++FG ++ K PA + R++ A+++ Sbjct: 61 MIGGTRANNLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESPANFKPRIEAAAKM 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 L + L R P LSGGQRQRVA+GRA+VR+ +FLFDEPLSNLDAKLR ++R EIK LH Sbjct: 121 LNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKALH 180 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 Q LKNT+IYVTHDQIEA+T+ADRI VM +G I+Q+ P+ +Y+ P NLFVA F+GSPSMN Sbjct: 181 QRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSMN 240 Query: 241 FFRGEVEPK---DGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGE 297 F G + + G + A G + PA + G KV LG+RPEH+ E Sbjct: 241 FAEGVLVNRTQGSGLALKLADGGEIVLEGAPASATV--GAKVTLGVRPEHI---ETITQT 295 Query: 298 PTHQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAES 357 P V++ EP GA+ L+ G + V + + PG V L +FD ES Sbjct: 296 PDVTMQVEVVEPTGAETHLYGKIGGDTWCVTTRQRSKVEPGERVTLRLPAAHIHLFDTES 355 Query: 358 ENRL 361 RL Sbjct: 356 GRRL 359 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: 363 Number of extensions: 14 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: 360 Length adjustment: 29 Effective length of query: 332 Effective length of database: 331 Effective search space: 109892 Effective search space used: 109892 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