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_000590982.1 HK29_RS06510 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_000382825.1:WP_000590982.1 Length = 247 Score = 120 bits (300), Expect = 3e-32 Identities = 74/226 (32%), Positives = 128/226 (56%), Gaps = 5/226 (2%) Query: 3 VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62 ++K+ NLS + + ++ ++ +GEVV+LIG++GAGK+T LR+L+ L P SG I+ Sbjct: 1 MIKISNLSKSFSGQTVLDHLNLDIQKGEVVALIGSSGAGKSTFLRSLNYLETPDSGSIQI 60 Query: 63 --LGQEIQKMPAQKIVA--GGLSQVPEGRHVFPGLTVMENLEMG-AFLKKNREENQANLK 117 + K+ ++I+A LS V + ++F T ++N++ G +KK ++ + Sbjct: 61 DDFSVDFSKITQEEILALRRKLSMVFQQFNLFERRTALDNVKEGLVVVKKLSDQEATKIA 120 Query: 118 KVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFD 177 K L +R+N LSGG++Q +A+ RAL P +LLLDEP+ L P + E+ Sbjct: 121 KEELAKVGLSDRENHYPRHLSGGQKQRVALARALAMKPDVLLLDEPTSALDPELVGEVEK 180 Query: 178 IIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKEL 223 I D K G T++L+ + + ++D+ L+ GKI+ SGT E+ Sbjct: 181 SIADAAKSGQTMILVSHDMSFVAQVADKILFLDKGKIIESGTPDEI 226 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: 123 Number of extensions: 6 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: 247 Length adjustment: 23 Effective length of query: 213 Effective length of database: 224 Effective search space: 47712 Effective search space used: 47712 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