Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__Pedo557:CA265_RS07485 Length = 252 Score = 126 bits (317), Expect = 5e-34 Identities = 75/201 (37%), Positives = 111/201 (55%), Gaps = 8/201 (3%) Query: 35 LKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQIDGVEVGHVAP------ 88 LK + LD+ GEFV +GPSG GKSTL+ + L+ +SG+ ++G V H++ Sbjct: 25 LKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGTYVLNGTNVSHMSDDALAEV 84 Query: 89 AKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLSLEPYLARRPA 148 + I VFQ++ L P T DN+ L L AG K + + + A+A + L + +P Sbjct: 85 RNQEIGFVFQTFNLLPRSTSLDNVALPLIYAGTSKKDRDARAARALENVGLGNRMDHKPN 144 Query: 149 ELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRSLKATMIYVTH 208 ELSGGQRQRVA+ RA++ P + L DEP NLD + + +H S T+I VTH Sbjct: 145 ELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIEIMGLLEEIH-SKGNTIILVTH 203 Query: 209 DQVEAMTLADKIVVLNAGRIE 229 ++ + A +IV + G IE Sbjct: 204 EE-DIAQHAHRIVRMRDGLIE 223 Lambda K H 0.320 0.137 0.393 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: 184 Number of extensions: 7 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: 352 Length of database: 252 Length adjustment: 26 Effective length of query: 326 Effective length of database: 226 Effective search space: 73676 Effective search space used: 73676 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