Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_000009985.1:WP_011385763.1 Length = 363 Score = 140 bits (353), Expect = 6e-38 Identities = 75/186 (40%), Positives = 117/186 (62%), Gaps = 9/186 (4%) Query: 34 LVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMNYR------VPQNRDIAMVFQDYALY 87 L G SG GK++ + M+AGL P G I + G + P+ R + VFQ++ L+ Sbjct: 28 LYGRSGSGKTSVINMVAGLSRPDEGSISVDGRVLFDSRSGIDLPPEARRLGYVFQEHRLF 87 Query: 88 PHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLLDRKPDELSGGQQQRVALGR 147 PH++VR N+ FG ++ SAER + + +V E LGI LLDR+P +LSGG++QRVA+GR Sbjct: 88 PHLSVRGNLEFG---QKLLPSAERTQSLDKVVELLGIESLLDRRPAKLSGGEKQRVAIGR 144 Query: 148 AIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTVYVTHNQTEAMTMADRIAV 207 A++ P + LMDEPL+ LD +AE+ + L + +V +YV+H+ E + +AD +A+ Sbjct: 145 ALLASPRILLMDEPLAALDPARKAEVLPFIAQLARRFSVPILYVSHSMDEVLRLADTLAL 204 Query: 208 MDDGEL 213 MD G++ Sbjct: 205 MDGGKV 210 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: 11 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: 363 Length adjustment: 30 Effective length of query: 353 Effective length of database: 333 Effective search space: 117549 Effective search space used: 117549 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