Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 5207560 Shew_0094 ABC transporter-related protein (RefSeq)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__PV4:5207560 Length = 369 Score = 154 bits (389), Expect = 4e-42 Identities = 89/213 (41%), Positives = 122/213 (57%), Gaps = 9/213 (4%) Query: 30 EFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG------GDHMNYRVPQNRDIAMVFQD 83 E L +VGPSG GKST +RM+AGL P SG+I G + Y PQ R + V Q Sbjct: 30 EVLAVVGPSGGGKSTLMRMIAGLTKPESGEIRYGDSVWFSSESGRYLTPQQRHLGYVPQH 89 Query: 84 YALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLLDRKPDELSGGQQQRV 143 + L+P+MT N+ L+ AER R + E + + L DR P LSGGQ+QRV Sbjct: 90 FGLFPNMTALANVVAALDH---IPKAERVARAKDWLERVNLHGLPDRLPANLSGGQRQRV 146 Query: 144 ALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTVYVTHNQTEAMTMAD 203 AL RA+ R+P V L+DEP S +D + R + EL L++QLA+ + VTH+ EA+ +AD Sbjct: 147 ALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKEQLAIPVIMVTHDLNEALLLAD 206 Query: 204 RIAVMDDGELQQVASPFECYHEPNNLFVAEFIG 236 R+ ++ G L Q SP E P N VA+ +G Sbjct: 207 RMILISQGTLLQQGSPREVLSRPRNEAVAKQMG 239 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: 288 Number of extensions: 13 Number of successful extensions: 3 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: 369 Length adjustment: 30 Effective length of query: 353 Effective length of database: 339 Effective search space: 119667 Effective search space used: 119667 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: 50 (23.9 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