Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_017557172.1 C892_RS0110655 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >NCBI__GCF_000341205.1:WP_017557172.1 Length = 281 Score = 184 bits (466), Expect = 2e-51 Identities = 102/254 (40%), Positives = 149/254 (58%), Gaps = 8/254 (3%) Query: 5 ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64 +L VE L++ FGGL A++ V V + VV LIGPNGAGKTTVFN ++G +P GT+ Sbjct: 7 VLAVEQLTVAFGGLTALDRVTFDVPHRSVVGLIGPNGAGKTTVFNAVSGVVRPRSGTLTR 66 Query: 65 DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLN---TNFFAGLFKTP 121 G P++ HH+ R G+ R Q + LF MT +EN+++ GL + P Sbjct: 67 HGRPLRRHRPHHLPRLGISRMLQGLGLFSGMTVLENVMVGADPLATGRLPGMLTGLGRAP 126 Query: 122 AFRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPA 181 + ER E AE L + + A+ GTL YG Q+R+ +AR + P +L+LDEPA Sbjct: 127 ---RDERRVRERAESALREFGVAHAAHALPGTLPYGVQKRVALARACVCGPELLLLDEPA 183 Query: 182 AGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQI 241 +GL+ E +L + +R +VLL+EH M LVM + D +VV++ G +ADGTP+++ Sbjct: 184 SGLSADEMSELAERVRAMRAYG--SVLLVEHHMDLVMRVCDRVVVLDFGRVIADGTPDEV 241 Query: 242 RDNPEVIKAYLGEA 255 R +P V +AYLG A Sbjct: 242 RADPAVERAYLGPA 255 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: 224 Number of extensions: 11 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: 281 Length adjustment: 25 Effective length of query: 230 Effective length of database: 256 Effective search space: 58880 Effective search space used: 58880 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 Sep 24 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