Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate Ga0059261_0562 Ga0059261_0562 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__Korea:Ga0059261_0562 Length = 232 Score = 121 bits (303), Expect = 2e-32 Identities = 77/207 (37%), Positives = 122/207 (58%), Gaps = 24/207 (11%) Query: 17 EVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDLTIDGMRV-----NDVA 71 E+++ I++DIA G V +GPSG GKS+LM +++GLE SGG++++ G+ + +A Sbjct: 28 EILKGIDVDIARGSSVAILGPSGSGKSSLMAILSGLERASGGEVSVAGIAYGTLDEDGLA 87 Query: 72 PAKRG-IAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKI--LHIDHLLD 128 A+RG + +V Q++ L P MT ++N+A L+LAG DA R A++ + + H L Sbjct: 88 RARRGRVGIVLQAFHLLPTMTAHENVAVPLELAGAP----DAFARAGAELDAVGLGHRLT 143 Query: 129 RKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALR---VKMRLEFARLHDELKT 185 P QLSGG++QRVAI RA+ +P++ DEP NLD A V + + R D Sbjct: 144 HYPVQLSGGEQQRVAIARAVAGRPEILFADEPTGNLDGATSGAIVDLLFDRQRAAD---A 200 Query: 186 TMIYVTHDQVEA------MTLADKIVV 206 T++ +THD A +T+ D ++V Sbjct: 201 TLLIITHDPALAERCDRVLTMRDGLIV 227 Lambda K H 0.320 0.135 0.384 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: 227 Number of extensions: 8 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: 369 Length of database: 232 Length adjustment: 26 Effective length of query: 343 Effective length of database: 206 Effective search space: 70658 Effective search space used: 70658 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: 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