Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate Ga0059261_0562 Ga0059261_0562 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Korea:Ga0059261_0562 Length = 232 Score = 112 bits (280), Expect = 1e-29 Identities = 68/203 (33%), Positives = 113/203 (55%), Gaps = 10/203 (4%) Query: 17 DVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGERV-----NDVP 71 +++ GID+DI G V +GPSG GKS+L+ +++GLE +GG++ + G + + Sbjct: 28 EILKGIDVDIARGSSVAILGPSGSGKSSLMAILSGLERASGGEVSVAGIAYGTLDEDGLA 87 Query: 72 PSKRG-IAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTPYLDRL 130 ++RG + +V Q++ L P MT ++N+A + +A + R D + L L Sbjct: 88 RARRGRVGIVLQAFHLLPTMTAHENVAVPLELA--GAPDAFARAGAELDAVGLGHRLTHY 145 Query: 131 PKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSDTTMIY 190 P LSGG++QRVAI RA+ P++ DEP NLD A A +++ +R +D T++ Sbjct: 146 PVQLSGGEQQRVAIARAVAGRPEILFADEPTGNLDGATSGAI-VDLLFDRQRAADATLLI 204 Query: 191 VTHDQVEAMTLADRIVVLSAGHI 213 +THD A DR++ + G I Sbjct: 205 ITHDPALA-ERCDRVLTMRDGLI 226 Lambda K H 0.320 0.137 0.387 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: 207 Number of extensions: 10 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: 362 Length of database: 232 Length adjustment: 26 Effective length of query: 336 Effective length of database: 206 Effective search space: 69216 Effective search space used: 69216 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