Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_000009985.1:WP_011385763.1 Length = 363 Score = 141 bits (355), Expect = 3e-38 Identities = 77/194 (39%), Positives = 120/194 (61%), Gaps = 10/194 (5%) Query: 39 LVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVL----NGVSA--QDRDIAMVFQSYALY 92 L G SG GK++ + M+AGL EG + ++ RVL +G+ + R + VFQ + L+ Sbjct: 28 LYGRSGSGKTSVINMVAGLSRPDEGSISVDGRVLFDSRSGIDLPPEARRLGYVFQEHRLF 87 Query: 93 PHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPGQLSGGQQQRVALGR 152 PH SVRGN+ FG + LP E Q +++ ++LGI LLDR+P +LSGG++QRVA+GR Sbjct: 88 PHLSVRGNLEFGQKL---LPSAERTQSLDKVVELLGIESLLDRRPAKLSGGEKQRVAIGR 144 Query: 153 AIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTHDQTEAMTMGDRVAV 212 A++ P + LMDEPL+ LD +AE+ + +L V +YV+H E + + D +A+ Sbjct: 145 ALLASPRILLMDEPLAALDPARKAEVLPFIAQLARRFSVPILYVSHSMDEVLRLADTLAL 204 Query: 213 LDDGELQQVGTPLD 226 +D G++ G PL+ Sbjct: 205 MDGGKVAASG-PLE 217 Lambda K H 0.316 0.136 0.384 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: 375 Number of extensions: 19 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: 42 (22.0 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