Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Dsui_0628 Dsui_0628 ABC-type branched-chain amino acid transport system, permease component
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__PS:Dsui_0628 Length = 358 Score = 414 bits (1063), Expect = e-120 Identities = 209/345 (60%), Positives = 261/345 (75%), Gaps = 16/345 (4%) Query: 13 VALLVLPLILQS-FGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71 + L VLP ++ + GNAW+RI + A+LY++LALGLNIVVG+AGLLDLGY+AFYAVGAYL+ Sbjct: 22 IVLAVLPFLVGAGLGNAWLRILNFAMLYIMLALGLNIVVGFAGLLDLGYIAFYAVGAYLY 81 Query: 72 ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131 AL+ASPH GLH +W ++P+ A++A GA+LGAPTL+LRGDYLAIV Sbjct: 82 ALLASPHF-------------GLHWPVWAILPLGAVVAGGAGALLGAPTLRLRGDYLAIV 128 Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYY 191 TLGFGEIIRIF+NNL+ PVN+TNGP+G+ ID V G+ L K L V G + S+ YYY Sbjct: 129 TLGFGEIIRIFMNNLNAPVNITNGPQGISSIDPFHVGGVTLAKPLSVLGVTVPSLHAYYY 188 Query: 192 LFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVS 251 LFL+L +V + + RL+DSRIGRAW+AIREDEIAAKA GIN RN+KLLAF MGA+FGGV+ Sbjct: 189 LFLLLALVIIFVTIRLEDSRIGRAWVAIREDEIAAKACGINVRNIKLLAFSMGATFGGVA 248 Query: 252 GAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPL 311 G +F +FQGFVSPESF LMES+M++ MVVLGG+GHIPGVILG +LL+ LPE R+ A PL Sbjct: 249 GGLFASFQGFVSPESFGLMESIMVLCMVVLGGMGHIPGVILGGILLTILPEAFRHAAVPL 308 Query: 312 QAMTDGR--LDSAILRQLLIALAMIIIMLLRPRGLWPSPEHGKSL 354 Q G+ +D LR LL LA+I +ML RP GLWPS + L Sbjct: 309 QKYAFGKVVVDPESLRMLLFGLALIAVMLYRPAGLWPSATRKREL 353 Lambda K H 0.328 0.144 0.430 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: 469 Number of extensions: 22 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 358 Length of database: 358 Length adjustment: 29 Effective length of query: 329 Effective length of database: 329 Effective search space: 108241 Effective search space used: 108241 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 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