Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Keio:17511 Length = 356 Score = 327 bits (837), Expect = 4e-94 Identities = 176/349 (50%), Positives = 236/349 (67%), Gaps = 8/349 (2%) Query: 14 GAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEEPK 73 G V+ L LD+ GEF+V++G SGCGKSTLL +AGL V++G I+I D+ VT EPK Sbjct: 15 GKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEGDIWINDQRVTEMEPK 74 Query: 74 DRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKRKPSE 133 DRGI MVFQ+YALYP M+VE+N+++GLK+ + +I +RVK A+ IL++ LLKR+P E Sbjct: 75 DRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAARILELDGLLKRRPRE 134 Query: 134 LSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMIYVTHD 193 LSGGQRQRVA+GRA+VRD VFLFDEPLSNLDAKLR ++R+E+++LH+ LK T +YVTHD Sbjct: 135 LSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQLHRRLKTTSLYVTHD 194 Query: 194 QIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVEPKDGRS 253 Q+EA+TLA R+ VM GV +Q+ P+ +Y P +LFVA FIGSP+MN G V +G Sbjct: 195 QVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPAMNLLTGRVN-NEGTH 253 Query: 254 FVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKV-DEARDGEPTHQAVVDIEEPMGA 312 F GGI + R G+K+ LG+RPEH+ + +A G P V+D E +GA Sbjct: 254 FELDGGIELPLN---GGYRQYAGRKMTLGIRPEHIALSSQAEGGVP---MVMDTLEILGA 307 Query: 313 DNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESENRL 361 DNL + Q + VR+A Q R GST+ L +FD E+ R+ Sbjct: 308 DNLAHGRWGEQKLVVRLAHQERPTAGSTLWLHLAENQLHLFDGETGQRV 356 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: 374 Number of extensions: 11 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