Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 209489 DVU0550 high-affinity branched-chain amino acid ABC transporter, ATP binding protein
Query= uniprot:Q1MCU2 (292 letters) >MicrobesOnline__882:209489 Length = 262 Score = 227 bits (578), Expect = 2e-64 Identities = 125/263 (47%), Positives = 165/263 (62%), Gaps = 6/263 (2%) Query: 13 TLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMIT 72 T+L V +S FGGL A+N+ G+I ALIGPNGAGKTT FNCITG Y PT G + Sbjct: 3 TVLDVRSISKNFGGLRALNEVDLRVDAGEIVALIGPNGAGKTTFFNCITGIYVPTEGEVV 62 Query: 73 FNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTI 132 + + + ++T E +ARTFQNIRLF +TVLEN+++ H + I Sbjct: 63 VTRPGSEPVRVNGQKPNQVT-ELGMARTFQNIRLFQNMTVLENVMIGCHCRTRSG----I 117 Query: 133 LG-LIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPE 191 LG L+ + E E I+ + L+ L + A +LPYGAQRRLEIARA+ T P Sbjct: 118 LGALLRDAKTRGEEQEIIDKSYELLKSVHLQQHYKEQARNLPYGAQRRLEIARALATNPF 177 Query: 192 LLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKI 251 LL LDEPAAG+NP+E+ L L+ IR S+LLIEHDM++VM +SD + V+EYG KI Sbjct: 178 LLLLDEPAAGMNPQETLELKGLVLEIRERLNLSVLLIEHDMNMVMSLSDRIYVMEYGSKI 237 Query: 252 SDGTPDHVKNDPRVIAAYLGVED 274 ++GTP+ V +PRVI AYLG E+ Sbjct: 238 AEGTPEEVSRNPRVIKAYLGEEE 260 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: 209 Number of extensions: 7 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: 262 Length adjustment: 25 Effective length of query: 267 Effective length of database: 237 Effective search space: 63279 Effective search space used: 63279 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