Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_041734471.1 BC1002_RS15605 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >NCBI__GCF_000092885.1:WP_041734471.1 Length = 258 Score = 219 bits (557), Expect = 5e-62 Identities = 114/238 (47%), Positives = 163/238 (68%), Gaps = 6/238 (2%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGS--PQAHS-GS 57 +L+ +++S YGK++ALH+ ++VR G+IV++IG NGAGKSTLL + G+ H+ G Sbjct: 15 ILEVDHLSVRYGKVEALHNAAIKVRAGQIVSVIGPNGAGKSTLLNAIMGALPTSGHAKGV 74 Query: 58 IRYMGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKG---DYQEQMD 114 I Y GE++ + + +VPE R +FA +TVE+NL +G + + ++ +Q++ Sbjct: 75 ISYQGEDVGAMPVEKRVALGMCLVPEKRELFASMTVEDNLLLGAYRRKRAGERNFLDQLE 134 Query: 115 KVLHLFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFD 174 V LFPRLKER Q GT+SGGE+QMLA+GRALM KP LL+LDEPSLGLAP+I+++IF Sbjct: 135 PVFELFPRLKERRKQAAGTLSGGERQMLAVGRALMGKPDLLMLDEPSLGLAPLIVKEIFH 194 Query: 175 IIEQLRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232 II LR+ GV L+EQNA AL+I+D YVLE G + ++G L +P+V E YLG Sbjct: 195 IISALRQTGVATLLIEQNARAALQISDYGYVLETGELALEGPAADLAQNPRVIETYLG 252 Lambda K H 0.320 0.137 0.381 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: 6 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: 233 Length of database: 258 Length adjustment: 24 Effective length of query: 209 Effective length of database: 234 Effective search space: 48906 Effective search space used: 48906 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: 46 (22.3 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