Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate Ga0059261_0562 Ga0059261_0562 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__Korea:Ga0059261_0562 Length = 232 Score = 115 bits (287), Expect = 2e-30 Identities = 77/219 (35%), Positives = 113/219 (51%), Gaps = 11/219 (5%) Query: 4 LELRNVNKTYGAGLPDT--LKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGA 61 + RNV T G T LK I++ I G + ++GPSG GKS+LM ++GLE +GG Sbjct: 11 IRARNVTLTLGTREAPTEILKGIDVDIARGSSVAILGPSGSGKSSLMAILSGLERASGGE 70 Query: 62 IMI-----GDQDVSGMSPKDRD-IAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAE 115 + + G D G++ R + +V Q++ L PTM+ EN+ L++ P D A Sbjct: 71 VSVAGIAYGTLDEDGLARARRGRVGIVLQAFHLLPTMTAHENVAVPLELAGAP--DAFAR 128 Query: 116 VARVAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMR 175 + + H L P QLSGG+QQRVA+ RA+A RP+I DEP NLD + Sbjct: 129 AGAELDAVGLGHRLTHYPVQLSGGEQQRVAIARAVAGRPEILFADEPTGNLDGATSGAIV 188 Query: 176 TEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGII 214 + + T + +THD A D+V M+DG+I Sbjct: 189 DLLFDRQRAADATLLIITHDPALAERC-DRVLTMRDGLI 226 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: 209 Number of extensions: 7 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: 232 Length adjustment: 27 Effective length of query: 359 Effective length of database: 205 Effective search space: 73595 Effective search space used: 73595 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: 48 (23.1 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