Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_002115805.1:WP_085638943.1 Length = 350 Score = 316 bits (810), Expect = 5e-91 Identities = 178/362 (49%), Positives = 241/362 (66%), Gaps = 14/362 (3%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M+ V++ + +G V+ ++LD+ GEF V +G SGCGKSTLL +AGL + ++G I Sbjct: 1 MSGVTLESVIKRYGQTQVIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEGTI 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 I R+VT +P DRG+ MVFQ+YALYP MTVE+N+ FGLK+ +I+++V AS I Sbjct: 61 RIGGRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEASRI 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 L++ LKRKP LSGGQRQRVAIGRA+VR +VFLFDEPLSNLDA+LR E+RVEI RLH Sbjct: 121 LKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARLH 180 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 + + TMIYVTHDQ+EA+TLAD+I V+++G I+Q+ PM +Y P+N FVAGFIGSPSMN Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPSMN 240 Query: 241 FFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTH 300 F RG V+ + V + G+ V+ + Q GQ+V++GLRPEH+ E R G +H Sbjct: 241 FIRGRVQGGE----VVSDGLVHSVSKTAS---AQEGQEVLIGLRPEHL---ELRPGS-SH 289 Query: 301 QAVVDIEEPMGADNLLWLTFA-GQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESEN 359 + VD+ E +G + L G+ + V G R G V L D +FDA++E Sbjct: 290 R--VDLTESLGGVSYAHLIGPDGEKIIVEERGDHRSSDGDMVDLVVDPDHMFLFDAKTEA 347 Query: 360 RL 361 RL Sbjct: 348 RL 349 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: 388 Number of extensions: 22 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: 350 Length adjustment: 29 Effective length of query: 332 Effective length of database: 321 Effective search space: 106572 Effective search space used: 106572 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 24 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