Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 136 bits (342), Expect = 9e-37 Identities = 80/222 (36%), Positives = 124/222 (55%), Gaps = 6/222 (2%) Query: 35 LKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQIDGVEVGHVAPA----- 89 L+ LD+ DGE +G SG GKSTL+R I LE + GS+ IDG E+ + A Sbjct: 21 LQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGSILIDGTEMTALGDAALRAQ 80 Query: 90 KRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKA-EIEEKVAKAAGMLSLEPYLARRPA 148 +R I M+FQ + L TV DN+ L+ AG A +I+ +V + + LE + ++ PA Sbjct: 81 RRRIGMIFQHFNLLSSQTVADNIAFPLRLAGETDAGKIKARVDELLRRVGLEAHASKYPA 140 Query: 149 ELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRSLKATMIYVTH 208 +LSGGQ+QRV I RA+ P + L DE S LD + +A ++R LK T++ +TH Sbjct: 141 QLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASVLELLAEINRELKLTIVLITH 200 Query: 209 DQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFI 250 + + D++ VL+AGRI + G+ +++ P + F+ Sbjct: 201 EMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTRRFV 242 Lambda K H 0.320 0.137 0.393 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: 275 Number of extensions: 11 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: 352 Length of database: 336 Length adjustment: 29 Effective length of query: 323 Effective length of database: 307 Effective search space: 99161 Effective search space used: 99161 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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