Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF3209 PGA1_c32620 high-affinity branched-chain amino acid transport ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__Phaeo:GFF3209 Length = 269 Score = 208 bits (529), Expect = 1e-58 Identities = 113/255 (44%), Positives = 161/255 (63%), Gaps = 3/255 (1%) Query: 4 KSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDA 63 K VV+++ I+ RFGG+ A+ D+ I+ G++ +IGPNGAGK++ NVI+G Y P Sbjct: 12 KIGGVVMEMKNITLRFGGVVAIKDISFDIREGEIRAIIGPNGAGKSSMLNVISGFYVPQE 71 Query: 64 GTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLF-GAVF 122 G GKP +EVA+ GIARTFQNI LF M+ L+NVM GR + +F A++ Sbjct: 72 GEVLFRGKPRPQMRPYEVARQGIARTFQNIALFDGMSVLDNVMTGRLNFMKTNIFQQAIW 131 Query: 123 RTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALD 182 R K +AEE + + ++D++ I L YG ++R+E+ARALA +P+L+ LD Sbjct: 132 RGKA-EAEETENREAVERIIDFLEIQAIRKTPVARLPYGLKKRVELARALAAEPKLLLLD 190 Query: 183 EPAAGMNATEKVQLRELIDRIRND-NRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNP 241 EP AGMN EK + I + ++ TI LIEHD+ +VM L DRV V+DYGK+I +G P Sbjct: 191 EPMAGMNVEEKEDMSRFILDVNDEFGTTIALIEHDMGVVMDLSDRVVVMDYGKKIGDGTP 250 Query: 242 AEVQKNEKVIEAYLG 256 EV+ N+ VI+AYLG Sbjct: 251 DEVRNNQDVIDAYLG 265 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: 190 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: 260 Length of database: 269 Length adjustment: 25 Effective length of query: 235 Effective length of database: 244 Effective search space: 57340 Effective search space used: 57340 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: 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