Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 169 bits (427), Expect = 2e-46 Identities = 95/234 (40%), Positives = 140/234 (59%), Gaps = 6/234 (2%) Query: 7 SNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISIDGK- 65 S I K+ G +K +L I GE V++G SG GKSTLLR + L SG + I+G Sbjct: 31 SEILKATGCTVAVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTD 90 Query: 66 --KIND---IEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120 K++D ++ + +++AMVFQ++ L PH +V N+ FGL+L+ + E ++ E +L Sbjct: 91 IAKVSDKELLQIRRKELAMVFQNFGLLPHRSVLHNIAFGLELQGVKKGEREQKAMESMQL 150 Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180 + +K ++ ELSGG +QRV L RAL+ V+L DE S LD +R QM+ E+ L Sbjct: 151 VGLKGYENQMVSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLTLQ 210 Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFI 234 K T++++THD EA LGDRIA++KDG I QIGT EI P N ++ F+ Sbjct: 211 SKMKKTIVFITHDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPANAYVERFV 264 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: 305 Number of extensions: 16 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: 408 Length adjustment: 30 Effective length of query: 317 Effective length of database: 378 Effective search space: 119826 Effective search space used: 119826 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: 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