Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate BWI76_RS26290 BWI76_RS26290 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Koxy:BWI76_RS26290 Length = 356 Score = 320 bits (819), Expect = 5e-92 Identities = 173/348 (49%), Positives = 232/348 (66%), Gaps = 8/348 (2%) Query: 14 GAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEEPK 73 G V+ L LD+ GEF+V++G SGCGKSTLL +AGL V+ G I+I + VT EPK Sbjct: 15 GKTQVIQPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTSGDIWIDRKRVTEMEPK 74 Query: 74 DRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKRKPSE 133 DRGI MVFQ+YALYP M+VE+N+++GLK+ + I +RV+ A+ IL++ LLKR+P E Sbjct: 75 DRGIAMVFQNYALYPHMSVEENMAWGLKIRGLGKGLIAERVQEAARILELDGLLKRRPRE 134 Query: 134 LSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMIYVTHD 193 LSGGQRQRVA+GRA+VRD VFLFDEPLSNLDAKLR ++R+E++ LH+ LK T +YVTHD Sbjct: 135 LSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQHLHRRLKTTSLYVTHD 194 Query: 194 QIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVEPKDGRS 253 Q+EA+TLA R+ VM GV +Q+ P+ +Y P + FVA FIGSP+MN G V DG Sbjct: 195 QVEAMTLAQRVMVMNKGVAEQIGTPVEVYEKPASRFVASFIGSPAMNLLEGRVS-DDGSR 253 Query: 254 FVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKV-DEARDGEPTHQAVVDIEEPMGA 312 F AGG+ + + R G+K+ LG+RPEH + +A G P V+D E +GA Sbjct: 254 FELAGGMLLPIN---SEHRRYAGRKMTLGIRPEHFALSSQAEGGVP---LVMDTLEILGA 307 Query: 313 DNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESENR 360 DNL + Q + VR+ Q+R GST+ L +FD+E+ R Sbjct: 308 DNLAHGRWGEQKLVVRLPHQQRPQAGSTLWLHLPQESLHLFDSETGQR 355 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: 384 Number of extensions: 13 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: 356 Length adjustment: 29 Effective length of query: 332 Effective length of database: 327 Effective search space: 108564 Effective search space used: 108564 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