Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate BWI76_RS07265 BWI76_RS07265 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >FitnessBrowser__Koxy:BWI76_RS07265 Length = 239 Score = 230 bits (586), Expect = 2e-65 Identities = 117/233 (50%), Positives = 168/233 (72%), Gaps = 1/233 (0%) Query: 3 VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62 +L V LSVHYG IQAVRDVSF V EGE +LIGANGAGK++ +R ++GL P SG+I F Sbjct: 4 LLTVNQLSVHYGGIQAVRDVSFSVKEGEQTTLIGANGAGKSSTVRAITGL-EPFSGEILF 62 Query: 63 LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFSR 122 G+ I+K A+ ++ GL VPEGR +F +TV+ENL+MGA+L+++ + + +F+ Sbjct: 63 NGKPIRKRRAESLLREGLVMVPEGRGIFARMTVLENLQMGAWLRRDAAAVKQEMGAIFAN 122 Query: 123 FPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQDI 182 FPRL ER++Q A LSGGEQQ+LA+ RAL+S P+LL+LDEPSMGLAP+ ++ IF +I + Sbjct: 123 FPRLAERQHQLAGLLSGGEQQLLALNRALLSQPRLLILDEPSMGLAPLMVENIFRVIATL 182 Query: 183 QKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235 +++G +LLIEQNA AL +D +V+++G IV G + L + + + + YLG Sbjct: 183 RQRGVALLLIEQNARLALEATDSAWVMDSGSIVERGPSQTLLADDRIAQIYLG 235 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: 171 Number of extensions: 7 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: 239 Length adjustment: 23 Effective length of query: 213 Effective length of database: 216 Effective search space: 46008 Effective search space used: 46008 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 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