Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__SB2B:6939439 Length = 370 Score = 147 bits (371), Expect = 5e-40 Identities = 84/213 (39%), Positives = 120/213 (56%), Gaps = 9/213 (4%) Query: 30 EFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG------GDHMNYRVPQNRDIAMVFQD 83 EFL +VGPSG GK+T LRM+AGL P +G I G D + PQNR I V Q Sbjct: 29 EFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRCGKRIWFDSDEGIHCSPQNRHIGFVPQH 88 Query: 84 YALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLLDRKPDELSGGQQQRV 143 + L+P ++ NI L+ S ER R + E + + L DR P +LSGGQ+QRV Sbjct: 89 FGLFPKLSALGNIMAALDH---LPSQERRPRALAALEKVNLHGLTDRLPSQLSGGQKQRV 145 Query: 144 ALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTVYVTHNQTEAMTMAD 203 AL RA+ R+P V L+DEP S +D + R + EL L+ +L + + VTH+ EA+ +AD Sbjct: 146 ALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAELNIPVIMVTHDLNEALLLAD 205 Query: 204 RIAVMDDGELQQVASPFECYHEPNNLFVAEFIG 236 + ++ G + Q +P + + P N VA +G Sbjct: 206 SMLLISQGHMLQHGTPQDVFSRPRNEAVARQMG 238 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: 282 Number of extensions: 12 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: 370 Length adjustment: 30 Effective length of query: 353 Effective length of database: 340 Effective search space: 120020 Effective search space used: 120020 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