Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >FitnessBrowser__Caulo:CCNA_02751 Length = 332 Score = 129 bits (323), Expect = 1e-34 Identities = 79/228 (34%), Positives = 124/228 (54%), Gaps = 17/228 (7%) Query: 14 GGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTLDGHLLN--GKS 71 GG A+ V+L + GE+ G+IG +GAGK+TL L+ G+ PS G V +DG + G + Sbjct: 14 GGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQVIVDGDDVAALGVA 73 Query: 72 PYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFYKSEKELKAK 131 + +G FQ+ L TV NV L+L + E+KA+ Sbjct: 74 GLRALRRRVGMIFQHFNLLSGKTVAQNVAFP-------------LKLAG--RPAAEVKAR 118 Query: 132 ALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGMNPQETAELT 191 ELL+ L A LS GQ++R+ I RALAT PK+L DE + ++P+ T ++ Sbjct: 119 TAELLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQIL 178 Query: 192 ELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEI 239 +LI + E +TI+LI H+M++V V +R+ VL+ GR++ +G +E+ Sbjct: 179 DLIAGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEV 226 Lambda K H 0.319 0.139 0.385 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: 221 Number of extensions: 11 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: 254 Length of database: 332 Length adjustment: 26 Effective length of query: 228 Effective length of database: 306 Effective search space: 69768 Effective search space used: 69768 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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