Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__SB2B:6938538 Length = 378 Score = 202 bits (513), Expect = 2e-56 Identities = 104/243 (42%), Positives = 161/243 (66%), Gaps = 2/243 (0%) Query: 4 VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIK 63 + + +S F V +D ++L I+ GE LLG SG GKSTLL +AG ++G+I++ Sbjct: 21 LKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYLD 80 Query: 64 DRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQI 123 +++T P +R I M+FQSYAL+P MTVE+N++FGLK K+ A+I +RV+ +++ + Sbjct: 81 GQDITDLPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDKMSKADISQRVQEMLKLVHM 140 Query: 124 QPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSL 183 + KRKP +LSGGQRQRVA+ R+L + + L DEP+ LD KLR+++++E+ + + + Sbjct: 141 EQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERV 200 Query: 184 KNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFR 243 T + VTHDQ EA+T+A RIA+M G I Q+ PM IY +P + +A FIG ++N F Sbjct: 201 GVTCVMVTHDQEEAMTMAGRIAIMSDGWIAQVGSPMDIYESPNSRMIAEFIG--TVNLFD 258 Query: 244 GEV 246 E+ Sbjct: 259 CEI 261 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: 314 Number of extensions: 9 Number of successful extensions: 1 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: 378 Length adjustment: 30 Effective length of query: 331 Effective length of database: 348 Effective search space: 115188 Effective search space used: 115188 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