Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate H281DRAFT_05513 H281DRAFT_05513 branched-chain amino acid transport system permease protein
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__Burk376:H281DRAFT_05513 Length = 597 Score = 193 bits (491), Expect = 6e-54 Identities = 101/249 (40%), Positives = 154/249 (61%), Gaps = 4/249 (1%) Query: 10 LKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELA 69 L V +SK++GG+ A+SDV ++ GQ++GLIGPNGAGK+T N+I G Y D+G L Sbjct: 346 LTVESVSKQYGGVLAVSDVSFSVAAGQIHGLIGPNGAGKSTLVNLIAGNYLCDSGRVRLD 405 Query: 70 GKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGS-GLFGAVFRTKGFK 128 G + AK G+ARTFQN++L + LENV++G G F + + F Sbjct: 406 GADVSNLVTADRAKRGLARTFQNLQLVEALPVLENVLLGMSSADGHVANFAKWWMGRAFD 465 Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188 E + A E+L + GI LSYG ++ +E+ARA+A P+L+ LDEP AG+ Sbjct: 466 LPER---REALEILAFFGIEHLCQAYPTELSYGHRKLVELARAIAQRPRLMLLDEPIAGL 522 Query: 189 NATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNE 248 N E +++ +++ R+R+ TILLIEH+++ VM LCD ++VL+ G+ I G P E++ +E Sbjct: 523 NGAEAMEVAKVVGRLRDAGVTILLIEHNMEFVMSLCDSISVLEQGRLIGTGTPEEIRSDE 582 Query: 249 KVIEAYLGT 257 +++ AYLGT Sbjct: 583 RILRAYLGT 591 Lambda K H 0.319 0.137 0.384 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: 389 Number of extensions: 16 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: 260 Length of database: 597 Length adjustment: 31 Effective length of query: 229 Effective length of database: 566 Effective search space: 129614 Effective search space used: 129614 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: 50 (23.9 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