Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 207786 DVU2299 glycine/betaine/L-proline ABC transporter, ATP binding protein
Query= uniprot:A8LLL2 (373 letters) >MicrobesOnline__882:207786 Length = 397 Score = 155 bits (392), Expect = 2e-42 Identities = 85/249 (34%), Positives = 144/249 (57%), Gaps = 9/249 (3%) Query: 23 NLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVNDVPP------AQRG 76 + D+++GE++V +G SG GKSTL+R + L + T GT+ +DG V +P QR Sbjct: 47 SFDVEEGEIVVVMGLSGSGKSTLVRCLNRLIEPTAGTVTVDGRDVTSMPVDELRRLRQRS 106 Query: 77 IAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKALSG 136 MVFQ++AL+PH TV +N +F L+ +AE + + E++ L ++ P LSG Sbjct: 107 FGMVFQNFALFPHRTVLQNAAFGLEAMGVPRAERERQAMVSLERVGLAEWAASRPAQLSG 166 Query: 137 GQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVTHDQV 196 G +QRV + R++ DP + L DE S LD +R + E+ +L++ + + T+V+++HD Sbjct: 167 GMQQRVGLARALSLDPDILLMDEAFSALDPLIRRDMQDELLRLQDDL-QKTIVFISHDLD 225 Query: 197 EAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMN--LLPGKIIGTGAQT 254 EA+ L RIV++ G + Q+G+P ++ P +++VA+F+G + L G ++ Sbjct: 226 EALKLGDRIVLMRDGAVVQIGTPEDILTNPADDYVARFVGEADVTKVLTAGSVMKRSEAV 285 Query: 255 TVEMTDGGR 263 V DG R Sbjct: 286 AVLGIDGPR 294 Lambda K H 0.316 0.135 0.379 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: 335 Number of extensions: 14 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: 373 Length of database: 397 Length adjustment: 30 Effective length of query: 343 Effective length of database: 367 Effective search space: 125881 Effective search space used: 125881 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 (21.6 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