Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Phaeo:GFF262 Length = 348 Score = 283 bits (724), Expect = 5e-81 Identities = 172/367 (46%), Positives = 230/367 (62%), Gaps = 30/367 (8%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 +T SVR + N V + + I+ GEF+VL+G SGCGKSTLL IAGL D+++G + Sbjct: 4 VTLNSVRKVYPN--GVEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEGTL 61 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 I DR V +P DR I MVFQ+YALYP MTV KN+++GLK K P AEI+++V A+++ Sbjct: 62 EIGDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQKVAEAAKM 121 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 L ++ L RKPS+LSGGQRQRVA+GRA+VRD +FLFDEPLSNLDAKLR+++R+EIK L Sbjct: 122 LNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKALQ 181 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 + L T IYVTHDQ+EA+T+ADRI V+ G I+Q+ P IY+ P ++FVA F+G+P MN Sbjct: 182 RRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPPMN 241 Query: 241 FF-----RGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARD 295 G+V DG S A D +A A V LG+RPE V++ A Sbjct: 242 LLDATIANGQVTLPDGVSMG-----ALDTSAQGA---------VKLGIRPEDVQL-VAEG 286 Query: 296 GEPTHQAVVDIE--EPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIF 353 G +D+E E +GA LL GQ ++ + PG T ++S D +F Sbjct: 287 G-----LAIDVELIEELGAHRLLHGKLGGQPFTIHVLKDIPVDPG-THQISVDPAAICLF 340 Query: 354 DAESENR 360 DAES R Sbjct: 341 DAESGQR 347 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: 373 Number of extensions: 17 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: 348 Length adjustment: 29 Effective length of query: 332 Effective length of database: 319 Effective search space: 105908 Effective search space used: 105908 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