Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_00010 (365 letters) >FitnessBrowser__Pedo557:CA265_RS07485 Length = 252 Score = 135 bits (340), Expect = 1e-36 Identities = 76/208 (36%), Positives = 119/208 (57%), Gaps = 8/208 (3%) Query: 12 GFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTIELDGRDITEVT 71 G E + +K + L++ EFV +GPSG GKSTL+ ++ L+ +SGT L+G +++ ++ Sbjct: 18 GSEVIHALKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGTYVLNGTNVSHMS 77 Query: 72 P------AKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARILELGS 125 +++ VFQT+ L P T N++ L AG K D + + A A + LG+ Sbjct: 78 DDALAEVRNQEIGFVFQTFNLLPRSTSLDNVALPLIYAGTSKKDRDARAARALENVGLGN 137 Query: 126 LLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLHKELQA 185 +D KP +LSGGQRQRVA+ RA++ NP I L DEP NLD ++ L +H + Sbjct: 138 RMDHKPNELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIEIMGLLEEIHSK-GN 196 Query: 186 TMIYVTHDQVEAMTLATKVVVLNAGRIE 213 T+I VTH++ + A ++V + G IE Sbjct: 197 TIILVTHEE-DIAQHAHRIVRMRDGLIE 223 Lambda K H 0.319 0.136 0.381 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: 203 Number of extensions: 5 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: 365 Length of database: 252 Length adjustment: 27 Effective length of query: 338 Effective length of database: 225 Effective search space: 76050 Effective search space used: 76050 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