Align glucose transporter, ATPase component (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF3641 (260 letters) >NCBI__GCF_000009985.1:WP_011385004.1 Length = 379 Score = 97.4 bits (241), Expect = 4e-25 Identities = 75/235 (31%), Positives = 113/235 (48%), Gaps = 22/235 (9%) Query: 12 ATPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGE 71 A PL+ + IS FG AV+HV + ++ GE LLG +G GK+TL+++L+G G Sbjct: 19 AVPLIRFEGISKRFGDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGR 78 Query: 72 IRVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRE---LVTPFGLVDDSA 128 I ++G V P + + ++Q+ AL ++ A N+ G + L P ++ D Sbjct: 79 ILIDGQDVTEVPPYE---RPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKP--VIKDKV 133 Query: 129 MEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGP-- 186 A M R + LSGGQRQ VA+AR + K++++DEP AAL Sbjct: 134 AAALELVQMGRFS------GRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKL 187 Query: 187 -HETQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNG---QLVGTVDI 237 TQ+ EL+ GI ++ HD M + R VM G Q+ VDI Sbjct: 188 REATQL--ELVNIQDRVGITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDI 240 Lambda K H 0.317 0.135 0.373 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: 183 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: 260 Length of database: 379 Length adjustment: 27 Effective length of query: 233 Effective length of database: 352 Effective search space: 82016 Effective search space used: 82016 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