Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Pedo557:CA265_RS07485 Length = 252 Score = 130 bits (328), Expect = 3e-35 Identities = 76/203 (37%), Positives = 116/203 (57%), Gaps = 9/203 (4%) Query: 18 AVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMNYRVP----- 72 A+ +SLDI+ EF+ L+GPSG GKST + +L L+TP+SG + G ++++ Sbjct: 24 ALKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGTYVLNGTNVSHMSDDALAE 83 Query: 73 -QNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLLDRK 131 +N++I VFQ + L P T N+ L G + +RD R E +G+ + +D K Sbjct: 84 VRNQEIGFVFQTFNLLPRSTSLDNVALPLIYA-GTSKKDRDARAARALENVGLGNRMDHK 142 Query: 132 PDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTVYV 191 P+ELSGGQ+QRVA+ RA++ +P + L DEP NLD K E+ L+ + + T + V Sbjct: 143 PNELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIEIMGLLEEIHSK-GNTIILV 201 Query: 192 THNQTEAMTMADRIAVMDDGELQ 214 TH + A A RI M DG ++ Sbjct: 202 THEEDIAQ-HAHRIVRMRDGLIE 223 Lambda K H 0.317 0.135 0.386 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: 197 Number of extensions: 4 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: 383 Length of database: 252 Length adjustment: 27 Effective length of query: 356 Effective length of database: 225 Effective search space: 80100 Effective search space used: 80100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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