Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC
Query= uniprot:Q6MNM2 (347 letters) >NCBI__GCF_000009985.1:WP_011385763.1 Length = 363 Score = 134 bits (338), Expect = 3e-36 Identities = 76/201 (37%), Positives = 121/201 (60%), Gaps = 9/201 (4%) Query: 22 IDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISIDGKKIND------IEPQNR 75 + L PG L G SG GK++++ +AGL D G+IS+DG+ + D + P+ R Sbjct: 17 VRLSAGPG-VTALYGRSGSGKTSVINMVAGLSRPDEGSISVDGRVLFDSRSGIDLPPEAR 75 Query: 76 DIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQIKHLLDRKPKELS 135 + VFQ + L+PH++V N+ FG KL L +AE T+ ++++ ELL I+ LLDR+P +LS Sbjct: 76 RLGYVFQEHRLFPHLSVRGNLEFGQKL--LPSAERTQSLDKVVELLGIESLLDRRPAKLS 133 Query: 136 GGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNSKSTMIYVTHDQM 195 GG++QRVA+GRAL ++L DEPL+ LD ++++ I +L ++YV+H Sbjct: 134 GGEKQRVAIGRALLASPRILLMDEPLAALDPARKAEVLPFIAQLARRFSVPILYVSHSMD 193 Query: 196 EATTLGDRIAVLKDGVIEQIG 216 E L D +A++ G + G Sbjct: 194 EVLRLADTLALMDGGKVAASG 214 Lambda K H 0.318 0.136 0.383 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: 297 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: 347 Length of database: 363 Length adjustment: 29 Effective length of query: 318 Effective length of database: 334 Effective search space: 106212 Effective search space used: 106212 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 (21.7 bits) S2: 49 (23.5 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