Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_011022097.1 MA_RS10955 daunorubicin resistance protein DrrA family ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >NCBI__GCF_000007345.1:WP_011022097.1 Length = 267 Score = 121 bits (303), Expect = 2e-32 Identities = 81/244 (33%), Positives = 125/244 (51%), Gaps = 17/244 (6%) Query: 3 REILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTI 62 + IL V++L+ +F L AV G++ V+ + A +GPNGAGK+T LT +PT G I Sbjct: 2 QNILSVKSLTKKFDDLTAVKGISFDVETGSIFAFLGPNGAGKSTTIKMLTTVLRPTSGEI 61 Query: 63 LLDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPA 122 L++G L AR FQ+ L ++TA EN+ + + ++K P Sbjct: 62 LING--YNALKEQDKARSSFGIVFQDYSLDSELTAYENM----------EYHSVIYKVP- 108 Query: 123 FRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182 K+ERE E + L+ V L N + G +RRLEIAR ++ P++L LDEP Sbjct: 109 --KAERE--ERIKTALEIVGLWNRRNDLVKKYSGGMKRRLEIARALVHYPKVLFLDEPTV 164 Query: 183 GLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIR 242 GL+P+ + I L EE +T+ L H M +++D I +I+ G + GT +I Sbjct: 165 GLDPQTRMSIWNHIKRLNEERKMTIFLTTHYMDEAEAMADKIAIIDHGKIIESGTLAEIM 224 Query: 243 DNPE 246 + E Sbjct: 225 ERTE 228 Lambda K H 0.321 0.138 0.398 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: 146 Number of extensions: 10 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: 255 Length of database: 267 Length adjustment: 25 Effective length of query: 230 Effective length of database: 242 Effective search space: 55660 Effective search space used: 55660 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 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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