Align ABC transporter for Lactose, ATPase component (characterized)
to candidate Ga0059261_0562 Ga0059261_0562 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__Korea:Ga0059261_0562 Length = 232 Score = 120 bits (300), Expect = 5e-32 Identities = 71/202 (35%), Positives = 110/202 (54%), Gaps = 9/202 (4%) Query: 17 EVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTIDDVRMNDVDP---- 72 E++KG+D+DI G V +GPSG GKS+L+ +++GLE S G++++ + +D Sbjct: 28 EILKGIDVDIARGSSVAILGPSGSGKSSLMAILSGLERASGGEVSVAGIAYGTLDEDGLA 87 Query: 73 -SKRG-IAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGALLDRK 130 ++RG + +V Q++ L P MT EN+ L AG P A R + LG L Sbjct: 88 RARRGRVGIVLQAFHLLPTMTAHENVAVPLELAGAPDA--FARAGAELDAVGLGHRLTHY 145 Query: 131 PKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLATTIVYV 190 P QLSGG++QRVAI RA+ P+I DEP NLD + + + T++ + Sbjct: 146 PVQLSGGEQQRVAIARAVAGRPEILFADEPTGNLDGATSGAIVDLLFDRQRAADATLLII 205 Query: 191 THDQVEAMTLADKIVVMRAGVV 212 THD A D+++ MR G++ Sbjct: 206 THDPALA-ERCDRVLTMRDGLI 226 Lambda K H 0.321 0.139 0.396 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: 203 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: 358 Length of database: 232 Length adjustment: 26 Effective length of query: 332 Effective length of database: 206 Effective search space: 68392 Effective search space used: 68392 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: 47 (22.7 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