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_028321172.1 H567_RS0109140 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_000422285.1:WP_028321172.1 Length = 244 Score = 255 bits (652), Expect = 5e-73 Identities = 124/234 (52%), Positives = 177/234 (75%) Query: 3 VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62 +L V + +YG I+A+R VS +VNEG++++L+G+NGAGKTT+L T+SGL+RP G+I F Sbjct: 7 LLDVLGVHSYYGRIRALRGVSLKVNEGDLITLMGSNGAGKTTLLNTISGLLRPGKGRIFF 66 Query: 63 LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFSR 122 + + +P KIV G++QVPEGR +F L+V+ENL++GAF++++R + ++ ++F Sbjct: 67 EERRLDGLPPHKIVKAGIAQVPEGRKIFGRLSVLENLDLGAFIRRDRSAVKEDMVRLFEL 126 Query: 123 FPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQDI 182 FPRL ER++Q A TLSGGEQQMLAMGRALM+ P+LLLLDEPSMGLAP+ ++ IFD I I Sbjct: 127 FPRLYERRHQTAGTLSGGEQQMLAMGRALMTRPRLLLLDEPSMGLAPLLVETIFDTITTI 186 Query: 183 QKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLGG 236 +G ++LL+EQNAN AL I+ RGYV++ G+IVL L +E V++ YLGG Sbjct: 187 NHRGCSILLVEQNANMALEITSRGYVIQNGEIVLEDQSTNLRGNEWVQRLYLGG 240 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: 182 Number of extensions: 2 Number of successful extensions: 1 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: 244 Length adjustment: 23 Effective length of query: 213 Effective length of database: 221 Effective search space: 47073 Effective search space used: 47073 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