Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 293 bits (750), Expect = 5e-84 Identities = 167/378 (44%), Positives = 240/378 (63%), Gaps = 30/378 (7%) Query: 1 MTSVSVRDLSLNF-GAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQ 59 M +S+R++ + G V V+ ++++I+ GEF+V++G SGCGKSTLL +AGL +S G+ Sbjct: 1 MAKLSLRNVQKTYAGNVKVVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAISGGE 60 Query: 60 IFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASE 119 + I D+ V EP +R I MVFQ+YALYP M+V N+++GLK+ + +EIE+RVK A+ Sbjct: 61 VHIGDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLKIRGMDKSEIEQRVKHAAG 120 Query: 120 ILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRL 179 IL++ PLL+RKP LSGGQRQRVA+GRA+VR+ VFLFDEPLSNLDAKLR ++R+E+K L Sbjct: 121 ILELAPLLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLELKEL 180 Query: 180 HQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSM 239 H+ L+ T +YVTHDQ+EA+TLADR+ V+ G ++Q+ P+ +Y P + FVA FIGSP M Sbjct: 181 HRRLRTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFIGSPPM 240 Query: 240 NFF--------RGE----VEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEH 287 N +GE VE K G A G + P L ++ +LGLRPEH Sbjct: 241 NLVPVTRTNGGQGEAQMRVEQKPG-----AQGAPATLGHLPMGLHLP--ERALLGLRPEH 293 Query: 288 VKVDEARDGEPTHQAVVDIE----EPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRL 343 ++ A H+A+ +IE E +GAD+ + T GQ + VR+ G + + Sbjct: 294 IEPCAA------HEAIAEIEVRLVEALGADSYAYGTLGGQPVVVRLDSNMPVSSGDRLPI 347 Query: 344 SFDMGVASIFDAESENRL 361 + FDA+S R+ Sbjct: 348 TAAAEHLHFFDADSGKRI 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: 393 Number of extensions: 18 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: 367 Length adjustment: 29 Effective length of query: 332 Effective length of database: 338 Effective search space: 112216 Effective search space used: 112216 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