Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF3209 PGA1_c32620 high-affinity branched-chain amino acid transport ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__Phaeo:GFF3209 Length = 269 Score = 202 bits (513), Expect = 9e-57 Identities = 107/262 (40%), Positives = 167/262 (63%), Gaps = 9/262 (3%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 ++++++++++FGG++AI D SF+ + G+I A+IGPNGAGK+++ N I+GFY P G + F Sbjct: 17 VMEMKNITLRFGGVVAIKDISFDIREGEIRAIIGPNGAGKSSMLNVISGFYVPQEGEVLF 76 Query: 74 NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133 K Q + + + ++ +ARTFQNI LF G++VL+N++ + N MK + + Sbjct: 77 RGKPRPQ-----MRPYEVARQG-IARTFQNIALFDGMSVLDNVMTGRLN-FMKTNIFQ-- 127 Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193 I G + E E E ++ ++ P LPYG ++R+E+ARA+ P+LL Sbjct: 128 QAIWRGKAEAEETENREAVERIIDFLEIQAIRKTPVARLPYGLKKRVELARALAAEPKLL 187 Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253 LDEP AG+N E ++ + + E GT+I LIEHDM VVM++SD VVV++YG+KI D Sbjct: 188 LLDEPMAGMNVEEKEDMSRFILDVNDEFGTTIALIEHDMGVVMDLSDRVVVMDYGKKIGD 247 Query: 254 GTPDHVKNDPRVIAAYLGVEDE 275 GTPD V+N+ VI AYLGV + Sbjct: 248 GTPDEVRNNQDVIDAYLGVSHD 269 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: 204 Number of extensions: 9 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: 269 Length adjustment: 26 Effective length of query: 266 Effective length of database: 243 Effective search space: 64638 Effective search space used: 64638 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