Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 203 bits (516), Expect = 7e-57 Identities = 106/236 (44%), Positives = 148/236 (62%), Gaps = 4/236 (1%) Query: 4 IQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISID 63 + + + +G+ L LDIA GEF+ L+GPSG GKS+LLR LAGL+ D G + D Sbjct: 3 LSIRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLRD 62 Query: 64 GKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAA----EITKRVNEISE 119 G + + Q RDI +VFQ YAL+PHMTVA+N+ FGL+++ A +I RV ++ Sbjct: 63 GTDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLLR 122 Query: 120 LLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRL 179 +Q++ L R P +LSGGQRQRVAL RAL+ + ++L DEP LDA +R +R+ ++ L Sbjct: 123 RVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRDL 182 Query: 180 HHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIG 235 + T + VTHDQ EA L DR+ V+ G IEQ+G PSEIY P F+ F+G Sbjct: 183 QRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVG 238 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: 8 Number of successful extensions: 2 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: 384 Length adjustment: 30 Effective length of query: 317 Effective length of database: 354 Effective search space: 112218 Effective search space used: 112218 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