Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_900115975.1:WP_092484009.1 Length = 344 Score = 207 bits (527), Expect = 4e-58 Identities = 102/217 (47%), Positives = 149/217 (68%) Query: 21 LKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIMIGDQDVSGMSPKDRDIA 80 L +I L ++EGE+ I++GP+G GK+ ++ IAG+ G I +++++ ++P+ R + Sbjct: 16 LLDINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLATLAPEQRKVG 75 Query: 81 MVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLLQIEHLLNRKPGQLSGGQ 140 V+Q YAL+P ++V+ENI FG +IRK+P+ I +++ + +L I HLLNR P LSGG+ Sbjct: 76 FVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLNRHPSTLSGGE 135 Query: 141 QQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQIEAM 200 QQR A+ RAL P+I L DEPLS LD + + + E+K +HQ LKTTT++VTHD EAM Sbjct: 136 QQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTLHVTHDFNEAM 195 Query: 201 TLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIG 237 L DK+ VM G I Q GTP+EI+ P N FVASF+G Sbjct: 196 YLADKIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVG 232 Lambda K H 0.318 0.135 0.382 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: 309 Number of extensions: 10 Number of successful extensions: 1 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: 344 Length adjustment: 29 Effective length of query: 357 Effective length of database: 315 Effective search space: 112455 Effective search space used: 112455 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 Apr 09 2024. 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