Align D-lactate transporter, ATP-binding component (characterized)
to candidate WP_067075333.1 MCUHO_RS06265 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF1248 (251 letters) >NCBI__GCF_001602375.1:WP_067075333.1 Length = 255 Score = 85.1 bits (209), Expect = 1e-21 Identities = 65/220 (29%), Positives = 107/220 (48%), Gaps = 13/220 (5%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 ++EV++V R G L DVNL+V ++ +AIIGPNG GK+TLL ++G L P G+V Sbjct: 5 VIEVEDVRVRLRGHTVLEDVNLTVHQDDFYAIIGPNGGGKTTLLRVILGLLQPSRGTVRI 64 Query: 63 DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQ 122 G G ++G F+T + ++V E ++ + R G + I G Sbjct: 65 LG----GTGAAARKELGYVPQFRTFDFEYPITVREMIL----SGRLG--HITRIPRRYGA 114 Query: 123 RDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMARA 182 D + E L M +AD +S G+++R I L +P++LLLDEPT + Sbjct: 115 ED-HARTEEALRMMGIADLADRQIRDLSGGEQQRAIIARALVGDPKVLLLDEPTVYVDAP 173 Query: 183 DTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVL 222 +L +++ + I ++ HD+ V+ R+ L Sbjct: 174 TAAQFYSILDRLRER--MAIVLVTHDIGVIPEHVTRVACL 211 Lambda K H 0.318 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: 170 Number of extensions: 7 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: 251 Length of database: 255 Length adjustment: 24 Effective length of query: 227 Effective length of database: 231 Effective search space: 52437 Effective search space used: 52437 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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