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_011780060.1 MVAN_RS14300 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_000015305.1:WP_011780060.1 Length = 253 Score = 260 bits (665), Expect = 2e-74 Identities = 133/235 (56%), Positives = 177/235 (75%), Gaps = 2/235 (0%) Query: 3 VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62 +L+V ++ VHYG I+A+ VS V+EGE+V+L+G+NGAGKTT++R +SGL+ SSG + F Sbjct: 17 LLEVRDVVVHYGRIKALHSVSLTVHEGELVTLLGSNGAGKTTMMRAISGLLPLSSGSVWF 76 Query: 63 LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKK--NREENQANLKKVF 120 G++I ++ A K VA GL Q PEGR VFPG+T++ENLEMG + +K ++ E+ L V Sbjct: 77 DGKDISRVKAHKRVADGLIQAPEGRGVFPGMTIVENLEMGCYGRKFPSKAEHDERLDWVL 136 Query: 121 SRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQ 180 FPRL ER+NQ TLSGGEQQMLA+GRALM+ PK+LLLDEPSMGLAP+ I +IF II Sbjct: 137 ETFPRLAERRNQVGGTLSGGEQQMLAIGRALMARPKVLLLDEPSMGLAPMVISQIFRIIA 196 Query: 181 DIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235 +I GTTVLL+EQNA +AL SDR Y+LETG++ +G +EL S + +R AYLG Sbjct: 197 EINAAGTTVLLVEQNAQQALTRSDRAYILETGEVTRTGNARELLSDKSIRAAYLG 251 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: 196 Number of extensions: 4 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: 253 Length adjustment: 24 Effective length of query: 212 Effective length of database: 229 Effective search space: 48548 Effective search space used: 48548 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