Align D-lactate transporter, ATP-binding component (characterized)
to candidate GFF1119 HP15_1097 branched-chain amino acid ABC transporter, ATP-binding protein
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__Marino:GFF1119 Length = 255 Score = 184 bits (466), Expect = 2e-51 Identities = 94/247 (38%), Positives = 153/247 (61%), Gaps = 4/247 (1%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 ILE +++ K +GG++AL D++L ++ +H ++GPNGAGKSTLLN L G L P +G + Sbjct: 6 ILETESLSKHWGGIKALDDISLQFQDKHLHGVVGPNGAGKSTLLNMLCGTLKPTSGCIFH 65 Query: 63 DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQ 122 G + G P+E GI R FQ I+ D++ LEN I + G+F N ++ Sbjct: 66 KGDQIEGMKPWEFVHRGIGRSFQKTNIYVDVTCLENCAIAAQRRFTGSF--NLFASRHSN 123 Query: 123 RDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMARA 182 + + E AE L ++ + ++ H AA +S G++R+LE+ M L+ +P +LLLDEP AGM Sbjct: 124 KLVREGAEKALCQVGLENRVHTVAAEISYGEQRQLELAMVLATDPCILLLDEPMAGMGHE 183 Query: 183 DTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGNPKV 242 ++ I+L+ Q+K + +I ++EHDM +F L+D++TVL GT L+ ++ + +V Sbjct: 184 ESQRIIELMNQLK--QTYSIVLVEHDMDAIFELSDQLTVLDNGTHLITGTVDEVRNDTRV 241 Query: 243 REAYLGE 249 +EAYLG+ Sbjct: 242 KEAYLGK 248 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: 169 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: 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 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