Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_000759345.1:WP_043527041.1 Length = 354 Score = 274 bits (701), Expect = 2e-78 Identities = 156/345 (45%), Positives = 216/345 (62%), Gaps = 18/345 (5%) Query: 1 MTSVSVRDLSLNF-GAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQ 59 M S+ + L + G V + ++L+I GEF+VL+G SGCGKSTLL +AGL ++DG Sbjct: 1 MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60 Query: 60 IFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASE 119 + I DR V EP +R I MVFQ+YALYP MTV NL++GLK + EIE+RV A+ Sbjct: 61 LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAA 120 Query: 120 ILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRL 179 +L+I+P L+RKP +LSGGQRQRVA+GRALVR+ FLFDEPLSNLDAKLR ++RVEIK+L Sbjct: 121 MLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQL 180 Query: 180 HQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSM 239 + LK T +YVTHDQ+EALTL DR+ V+ G I+Q+ PM +Y P ++FVA FIGSP+M Sbjct: 181 QRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAM 240 Query: 240 NFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPT 299 N + G A G+ + A V+G+RP+ ++++ + Sbjct: 241 NMLPVAYLRERG-----ANGLLDHLAA----------DTDVIGIRPDDLRIEAPDEDHLV 285 Query: 300 HQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYP--PGSTVR 342 V++ E GA++ L+++ G I R P G T+R Sbjct: 286 VTGTVELFEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMR 330 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: 339 Number of extensions: 8 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: 354 Length adjustment: 29 Effective length of query: 332 Effective length of database: 325 Effective search space: 107900 Effective search space used: 107900 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