Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 350388 BT0860 putative ABC transporter ATP-binding protein (NCBI ptt file)
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Btheta:350388 Length = 224 Score = 115 bits (289), Expect = 8e-31 Identities = 77/201 (38%), Positives = 115/201 (57%), Gaps = 10/201 (4%) Query: 19 LDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLD-VSDGQIFIKDRNVTWEEPKDRG- 76 L+ +++++ GEF+ ++G SGCGKSTLLN I GLLD + G+ ++ V+ R Sbjct: 21 LNNVSIEVKQGEFVAIMGPSGCGKSTLLN-ILGLLDNPTGGEYYLNGTEVSKYTESQRTS 79 Query: 77 -----IGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKRKP 131 IG VFQS+ L ++ V +N+ L I +E +KRV+ A E + I K P Sbjct: 80 LRKGVIGFVFQSFNLIDELNVYENIELPLLYMGISASERKKRVETAMERMAITHRSKHFP 139 Query: 132 SELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMIYVT 191 +LSGGQ+QRVAI RA+V + + L DEP NLD+K E+ + L++ T++ VT Sbjct: 140 QQLSGGQQQRVAIARAVVANPKLILADEPTGNLDSKNGKEVMGLLSELNKE-GTTIVMVT 198 Query: 192 HDQIEALTLADRIAVMKSGVI 212 H Q +A ADRI + G + Sbjct: 199 HSQHDA-GYADRIINLFDGQV 218 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: 182 Number of extensions: 10 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: 224 Length adjustment: 26 Effective length of query: 335 Effective length of database: 198 Effective search space: 66330 Effective search space used: 66330 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: 47 (22.7 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