Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 126 bits (316), Expect = 9e-34 Identities = 78/241 (32%), Positives = 129/241 (53%), Gaps = 10/241 (4%) Query: 4 IQFSNIKKSFG----SADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGT 59 I+F ++ KS+ L+ LDIA GE ++G SG GKSTL+R + LE G+ Sbjct: 2 IRFVDVHKSYRVDGKDIPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGS 61 Query: 60 ISIDGKKINDI-----EPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLA-AAEITKR 113 I IDG ++ + Q R I M+FQ + L TVA+N+ F L+L A +I R Sbjct: 62 ILIDGTEMTALGDAALRAQRRRIGMIFQHFNLLSSQTVADNIAFPLRLAGETDAGKIKAR 121 Query: 114 VNEISELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMR 173 V+E+ + ++ + P +LSGGQ+QRV + RAL+ + ++L DE S LD + + Sbjct: 122 VDELLRRVGLEAHASKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASVL 181 Query: 174 LEIKRLHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATF 233 + ++ K T++ +TH+ + DR+AVL G I + G ++++ P++ F Sbjct: 182 ELLAEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTRRF 241 Query: 234 I 234 + Sbjct: 242 V 242 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: 234 Number of extensions: 9 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: 347 Length of database: 336 Length adjustment: 29 Effective length of query: 318 Effective length of database: 307 Effective search space: 97626 Effective search space used: 97626 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