Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate AO356_28585 AO356_28585 ABC transporter
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28585 Length = 379 Score = 300 bits (767), Expect = 5e-86 Identities = 164/355 (46%), Positives = 225/355 (63%), Gaps = 25/355 (7%) Query: 3 KIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISI 62 K++ N+ K G A +L+ + L+I+ GEF+V VGPSGCGKSTLLR +AGL+S G + I Sbjct: 3 KLKLDNVNKQLGGARILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLI 62 Query: 63 DGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQ 122 DG+++ND+EP+ R + MVFQSYALYPHM+V +N+ FGLKL + +RV + +++LQ Sbjct: 63 DGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKTSLRERVLKTAQILQ 122 Query: 123 IKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHN 182 + LL RKP+ELSGGQRQRVA+GRA++R+ ++LFDEPLSNLDA LR QMR EI RLH Sbjct: 123 LDKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHGR 182 Query: 183 SKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFL 242 STMIYVTHDQ+EA TL D+I VL G IEQ+G+P E+Y RP + F+A F+GSP MNFL Sbjct: 183 LGSTMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYERPASRFVAGFLGSPRMNFL 242 Query: 243 -------------EGAVLEKIPWP-----EARKADQILGIRPDAFALNQGPLGTQEVALG 284 E VL P A LGIRP+ AL + GT +A+ Sbjct: 243 AAFLHTPGETSQVESLVLGMTSLPFDSSGLAANTQLSLGIRPEHIAL-KAAQGTAGIAVS 301 Query: 285 DFQIDISENLGGQQMLHGTLAGNNVRILVDSMD-NFSMKQTLPLKIDLTKAHLFD 338 E LG + +H ++ + ++ + + + L++D+ H+FD Sbjct: 302 GV-----EYLGSETYVHLDTGQDDPMVCRCEVNAGWRVGDRVELQLDIDNLHVFD 351 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: 351 Number of extensions: 14 Number of successful extensions: 1 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: 379 Length adjustment: 29 Effective length of query: 318 Effective length of database: 350 Effective search space: 111300 Effective search space used: 111300 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