Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate H281DRAFT_04059 H281DRAFT_04059 amino acid/amide ABC transporter ATP-binding protein 2, HAAT family
Query= TCDB::Q8DQH7 (236 letters) >FitnessBrowser__Burk376:H281DRAFT_04059 Length = 240 Score = 249 bits (637), Expect = 3e-71 Identities = 117/234 (50%), Positives = 180/234 (76%) Query: 2 SVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIE 61 ++LK++ L V+YG IQAV+ + EV +GE+V+LIGANGAGKTT ++ ++GL ++G IE Sbjct: 6 AMLKIKGLQVNYGGIQAVKGIDLEVGQGELVTLIGANGAGKTTTMKAITGLKPYAAGDIE 65 Query: 62 FLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFS 121 ++GQ I+ +P +++ GL+ VPEGR +F ++++EN++MGA+L+ + + +A++ ++F Sbjct: 66 YMGQSIKGVPPHELLKRGLAMVPEGRGIFARMSIVENMQMGAYLRSDNDGIKADVDRMFG 125 Query: 122 RFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQD 181 FPRL+ER Q A TLSGGEQQMLAM RA++S PKLLLLDEPSMGL+PI +++IF++++ Sbjct: 126 FFPRLKERATQYAGTLSGGEQQMLAMARAIISRPKLLLLDEPSMGLSPIMVEKIFEVVRA 185 Query: 182 IQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235 I +G TVLL+EQNA AL ++RGYV+++G + +SG K++ +VR AYLG Sbjct: 186 ISAEGMTVLLVEQNARLALQAANRGYVMDSGLVTMSGDAKQMLDDPKVRAAYLG 239 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: 168 Number of extensions: 7 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: 240 Length adjustment: 23 Effective length of query: 213 Effective length of database: 217 Effective search space: 46221 Effective search space used: 46221 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