Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_013529094.1 MESCI_RS06155 ATP-binding cassette domain-containing protein
Query= uniprot:A0A159ZWS6 (255 letters) >NCBI__GCF_000185905.1:WP_013529094.1 Length = 518 Score = 261 bits (666), Expect = 3e-74 Identities = 136/262 (51%), Positives = 182/262 (69%), Gaps = 9/262 (3%) Query: 1 MSREILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGG 60 M+ IL+V++LSM+FGGL+A+ ++ K ++ ALIGPNGAGKTTVFNC+TGFY+P+ G Sbjct: 13 MNDAILQVDHLSMKFGGLVAIGDLSFAAKRGEITALIGPNGAGKTTVFNCITGFYKPSEG 72 Query: 61 TILL---DGEP--IQGLPGHHI-ARKGVVRTFQNVRLFKDMTAVENLLIAQHRHL---NT 111 I L DG ++ LP H I AR V RTFQN+RLF MT +ENLL+AQH L + Sbjct: 73 MITLNRNDGSTFLLERLPNHEIPARAKVARTFQNIRLFSGMTLLENLLVAQHNKLMKASG 132 Query: 112 NFFAGLFKTPAFRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTR 171 GLF +RK+ E++E A++WL+K +L + A+ PAG L YG QRRLEIAR M T Sbjct: 133 YTVLGLFGFSGYRKASAESVELAKHWLEKADLVDRADDPAGDLPYGAQRRLEIARAMCTG 192 Query: 172 PRILMLDEPAAGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGT 231 P +L LDEPAAGLNPKE+ L L+ ++ ++LLIEHDM +VM ISDH+VV+ G Sbjct: 193 PELLCLDEPAAGLNPKESAALNELLIDIKNTSGASILLIEHDMSVVMQISDHVVVLEYGR 252 Query: 232 PLADGTPEQIRDNPEVIKAYLG 253 ++DG+P+ +R +P VI AYLG Sbjct: 253 KISDGSPQSVRTDPRVIAAYLG 274 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: 303 Number of extensions: 9 Number of successful extensions: 3 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: 518 Length adjustment: 29 Effective length of query: 226 Effective length of database: 489 Effective search space: 110514 Effective search space used: 110514 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: 49 (23.5 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