Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF1248 PGA1_c12640 putative high-affinity branched-chain amino acid transport ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__Phaeo:GFF1248 Length = 251 Score = 150 bits (379), Expect = 3e-41 Identities = 89/258 (34%), Positives = 143/258 (55%), Gaps = 12/258 (4%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 +L+V+++ +FGGL A++D + + + A+IGPNGAGK+T+ NC+ G P G + F Sbjct: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 Query: 74 NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133 + KS +L R P + I + ++R FQ +F L+VLEN+++ K G + Sbjct: 63 DGKS----VLGRAP-YEINQMG-ISRVFQTPEIFGDLSVLENMMIPC---FAKRDGAFEM 113 Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193 I +R+ +E A LE+ ++ D+ A + G +RRLEI + P LL Sbjct: 114 NAISAVSGQRDI---LEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLL 170 Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253 LDEP AG+ ++ LLK I++E +I +IEHDM VV ++D + VL G + + Sbjct: 171 LLDEPTAGMARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVE 230 Query: 254 GTPDHVKNDPRVIAAYLG 271 P ++K +P+V AYLG Sbjct: 231 DDPQNIKGNPKVREAYLG 248 Lambda K H 0.318 0.136 0.386 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: 202 Number of extensions: 12 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: 292 Length of database: 251 Length adjustment: 25 Effective length of query: 267 Effective length of database: 226 Effective search space: 60342 Effective search space used: 60342 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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