Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 131 bits (330), Expect = 2e-35 Identities = 96/292 (32%), Positives = 149/292 (51%), Gaps = 29/292 (9%) Query: 8 NVNKTY---GPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILV 64 +V+K+Y G +P L+ L I DGE ++G SG GKSTL+ I LE SGG+IL+ Sbjct: 6 DVHKSYRVDGKDIP-ALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGSILI 64 Query: 65 DDADISGMSP-----KDRDIAMVFQSYALYPTMSVRDNIAFGLKIR-KMPTAEIDEEVAR 118 D +++ + + R I M+FQ + L + +V DNIAF L++ + +I V Sbjct: 65 DGTEMTALGDAALRAQRRRIGMIFQHFNLLSSQTVADNIAFPLRLAGETDAGKIKARVDE 124 Query: 119 VSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEM 178 + + + +E S+ P QLSGGQ+QRV + RALA RP I L DE S LD + + + Sbjct: 125 LLRRVGLEAHASKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASVLELL 184 Query: 179 KLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGS 238 +++ LK T V +TH+ + D+VAV+ G I + G D++ +P + F+ Sbjct: 185 AEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTRRFVNE 244 Query: 239 ----------PPMNFIPLRLQRKDGRLLALLDSGQARCELPLG--MQDAGLE 278 P +P GR+L L G+A LG +D G++ Sbjct: 245 ALPEEAAGELAPYTHVP-------GRILRLSFRGEATWTPALGRVARDTGVD 289 Lambda K H 0.319 0.138 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: 302 Number of extensions: 15 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: 386 Length of database: 336 Length adjustment: 29 Effective length of query: 357 Effective length of database: 307 Effective search space: 109599 Effective search space used: 109599 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 (21.7 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