Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate 209027 DVU0098 polyamine ABC transporter, ATP-binding protein (TIGR)
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__DvH:209027 Length = 368 Score = 218 bits (554), Expect = 3e-61 Identities = 115/259 (44%), Positives = 165/259 (63%), Gaps = 6/259 (2%) Query: 4 LELRNVNKTYGAGLPDT--LKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGA 61 +ELR V K + DT L NI+L I+ GEFL L+GPSGCGK+T++ I+G E G Sbjct: 8 IELRGVTKNF----EDTCALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGV 63 Query: 62 IMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAK 121 I + Q + P+ R + VFQ+YAL+P MSVREN+ FGL++++ P+ +I V + Sbjct: 64 ITLKGQRMDDAPPEARQVNTVFQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALR 123 Query: 122 LLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLM 181 ++ +E +R+P QLSGGQQQRVA+ RA+ P + L DEP S LD KLR +M+ E+K + Sbjct: 124 MVHLEAHADRRPRQLSGGQQQRVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHL 183 Query: 182 HQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPM 241 ++L T V+VTHDQ EA + D+V VM DG I+Q G+P+EIY PAN +VA F+G + Sbjct: 184 QRQLGITFVFVTHDQEEAFAMSDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFVGEINI 243 Query: 242 NFVPLRLQRKDGRLVALLD 260 + DG A+++ Sbjct: 244 LNAVIAANHGDGLYDAVIE 262 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: 366 Number of extensions: 9 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: 368 Length adjustment: 30 Effective length of query: 356 Effective length of database: 338 Effective search space: 120328 Effective search space used: 120328 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: 50 (23.9 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