Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_012965674.1 FERP_RS05850 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_000025505.1:WP_012965674.1 Length = 238 Score = 186 bits (471), Expect = 5e-52 Identities = 90/218 (41%), Positives = 152/218 (69%), Gaps = 2/218 (0%) Query: 3 VLKVENLSVHYGM-IQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIE 61 +L+VENLS Y I + VS EV +G + S++G NG+GK+T+L+T+ G ++P SG++ Sbjct: 1 MLRVENLSSGYHKDINVLNGVSLEVKKGTITSVLGPNGSGKSTLLKTIYGYLKPFSGRVI 60 Query: 62 FLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFL-KKNREENQANLKKVF 120 + G+++ +P + + G++ + + +F LTV ENL+ G ++ +KN+E + LK V+ Sbjct: 61 YNGEDVTNLPPHEKIKKGIAYISQEHGIFHSLTVEENLKAGMWIYRKNKELVKEKLKAVY 120 Query: 121 SRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQ 180 RFP L+E++N A LSGG+Q++L AL+S P+L+L+DEP+ GL+PI +E+++I++ Sbjct: 121 DRFPILKEKRNVKAGFLSGGQQKLLQFSVALLSNPELILVDEPTAGLSPIASEEVYEILK 180 Query: 181 DIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSG 218 +++++G T+LL+EQN KA+ +SD YVLE GKI G Sbjct: 181 ELKREGKTILLVEQNLRKAIEVSDFAYVLELGKIRYGG 218 Lambda K H 0.315 0.134 0.358 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: 166 Number of extensions: 11 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: 236 Length of database: 238 Length adjustment: 23 Effective length of query: 213 Effective length of database: 215 Effective search space: 45795 Effective search space used: 45795 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: 42 (22.0 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