Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate AO353_25130 AO353_25130 ABC transporter
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25130 Length = 381 Score = 296 bits (757), Expect = 8e-85 Identities = 159/357 (44%), Positives = 223/357 (62%), Gaps = 25/357 (7%) Query: 1 MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60 M K++ N+ K G +L+ + L+IA GEF+V VGPSGCGKSTLLR +AGL+S +G + Sbjct: 1 MIKLKLDNVNKQLGGVRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICAGDL 60 Query: 61 SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120 ID +++ND+EP+ R + MVFQSYALYPHM+V +N+ FGLKL + + +RV +++ Sbjct: 61 LIDERRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKSSLRERVLRTAQI 120 Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180 LQ+ LL RKPKELSGGQRQRVA+GRA++R+ ++LFDEPLSNLDA LR QMR EI RLH Sbjct: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240 STMIYVTHDQ+EA TL D+I VL G +EQ+G+P E+Y RP + F+A F+GSP MN Sbjct: 181 ARLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 Query: 241 FLEGAV---------------LEKIPWPEARKADQI---LGIRPDAFALNQGPLGTQEVA 282 FL + + +P+ + A LG+RP+ +L + Sbjct: 241 FLAARLHAPGETSLVDTPVLGMTSLPFDSSNLAADTPLSLGVRPEHVSLKAADGTVGVIV 300 Query: 283 LGDFQIDISENLGGQQMLHGTLAGNNVRILVDSMD-NFSMKQTLPLKIDLTKAHLFD 338 G E LG + +H ++ I ++ + + + L++D+ HLFD Sbjct: 301 TG------VEYLGSETYVHLDTGQDDPLICRCEVNAGWQVGDRVELQLDIGNLHLFD 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: 365 Number of extensions: 12 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: 381 Length adjustment: 29 Effective length of query: 318 Effective length of database: 352 Effective search space: 111936 Effective search space used: 111936 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