Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate Ga0059261_0562 Ga0059261_0562 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Korea:Ga0059261_0562 Length = 232 Score = 108 bits (269), Expect = 2e-28 Identities = 63/184 (34%), Positives = 107/184 (58%), Gaps = 9/184 (4%) Query: 17 KVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVV-----NDVP 71 ++L I++DI +G + +GPSG GKS+L+ +++GLE+ +GG + + G + + Sbjct: 28 EILKGIDVDIARGSSVAILGPSGSGKSSLMAILSGLERASGGEVSVAGIAYGTLDEDGLA 87 Query: 72 PAQRG-IAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRL 130 A+RG + +V Q++ L P MT EN++ L++A A A E A + LG L Sbjct: 88 RARRGRVGIVLQAFHLLPTMTAHENVAVPLELAGAPDAFARAGAELDA--VGLGHRLTHY 145 Query: 131 PKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVY 190 P LSGG++QRVAI R++ P++ DEP NLD A A +++ ++ ++T++ Sbjct: 146 PVQLSGGEQQRVAIARAVAGRPEILFADEPTGNLDGATSGAI-VDLLFDRQRAADATLLI 204 Query: 191 VTHD 194 +THD Sbjct: 205 ITHD 208 Lambda K H 0.316 0.135 0.379 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: 226 Number of extensions: 15 Number of successful extensions: 2 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: 373 Length of database: 232 Length adjustment: 26 Effective length of query: 347 Effective length of database: 206 Effective search space: 71482 Effective search space used: 71482 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 (21.6 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