Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Pedo557:CA265_RS07485 Length = 252 Score = 123 bits (309), Expect = 5e-33 Identities = 77/204 (37%), Positives = 116/204 (56%), Gaps = 8/204 (3%) Query: 16 VTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTW------ 69 + L ++LDI+ GEF+ L+G SG GKSTL+N + L S G + NV+ Sbjct: 22 IHALKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGTYVLNGTNVSHMSDDAL 81 Query: 70 EEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKR 129 E +++ IG VFQ++ L P+ T N++ L A + + R RA E + + + Sbjct: 82 AEVRNQEIGFVFQTFNLLPRSTSLDNVALPLIYAGTSKKDRDARAARALENVGLGNRMDH 141 Query: 130 KPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMIY 189 KP+ELSGGQRQRVA+ RAL+ + + L DEP NLD K E+ ++ +H S NT+I Sbjct: 142 KPNELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIEIMGLLEEIH-SKGNTIIL 200 Query: 190 VTHDQIEALTLADRIAVMKSGVIQ 213 VTH++ + A RI M+ G+I+ Sbjct: 201 VTHEE-DIAQHAHRIVRMRDGLIE 223 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: 205 Number of extensions: 8 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: 252 Length adjustment: 27 Effective length of query: 334 Effective length of database: 225 Effective search space: 75150 Effective search space used: 75150 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: 48 (23.1 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