Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 130 bits (326), Expect = 6e-35 Identities = 84/232 (36%), Positives = 125/232 (53%), Gaps = 12/232 (5%) Query: 18 ALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGGRDVTTVEPAD--- 74 AL +LDI DGE +G SG GKSTL+R + LE S G I I G ++T + A Sbjct: 20 ALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGSILIDGTEMTALGDAALRA 79 Query: 75 --RDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRK--ERIAEAARVLQLEDYLDRK 130 R + M+FQ + L TV +N+ F +++ G E D K R+ E R + LE + + Sbjct: 80 QRRRIGMIFQHFNLLSSQTVADNIAFPLRLAG-ETDAGKIKARVDELLRRVGLEAHASKY 138 Query: 131 PGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMIYV 190 P QLSGGQ+QRV I RA+ PS+ L DE S LD + + L ++++L T++ + Sbjct: 139 PAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASVLELLAEINRELKLTIVLI 198 Query: 191 THDQVEAMTMADKIVVLNRGRIEQVGSPMDLY----HKPNSRFVAEFIGSPA 238 TH+ + D++ VL+ GRI + G+ D++ H RFV E + A Sbjct: 199 THEMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTRRFVNEALPEEA 250 Lambda K H 0.320 0.139 0.396 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: 18 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: 338 Length of database: 336 Length adjustment: 28 Effective length of query: 310 Effective length of database: 308 Effective search space: 95480 Effective search space used: 95480 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