Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate GFF2933 HP15_2877 ABC transporter, urea, ATP-binding protein, UrtE
Query= uniprot:A0A159ZWL6 (233 letters) >FitnessBrowser__Marino:GFF2933 Length = 232 Score = 166 bits (419), Expect = 5e-46 Identities = 98/230 (42%), Positives = 143/230 (62%), Gaps = 4/230 (1%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60 ML+ E ++ FYG+ L ++++V QG+ ++G NG GK+TL+ + G +GSI + Sbjct: 1 MLKIEKLNQFYGESHTLWDLDLDVPQGQCTCVMGRNGVGKTTLMKCIMGEETTKNGSIEF 60 Query: 61 MGE-ELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKGDYQEQMDKVLHL 119 G+ EL + R I VP+GR++F LTVEENL G K ++ ++V L Sbjct: 61 AGDVELTKKKVEDRSRLGIGYVPQGRQIFPLLTVEENLRTG-LAVRKDGSKKIPERVYEL 119 Query: 120 FPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQL 179 FP LKE +RGG +SGG+QQ LAIGRAL+ +P+LL+LDEP G+ P I+ QI ++I +L Sbjct: 120 FPVLKEMRHRRGGDLSGGQQQQLAIGRALVIEPRLLILDEPGEGIQPNIVAQIGEVIRKL 179 Query: 180 -RKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVRE 228 +DG+TV LVEQ A K ADR +L+ GR V +G A LTD +++ Sbjct: 180 IEEDGLTVLLVEQKLPFARKYADRFAILDRGRRVAEGE-IAGLTDELIKK 228 Lambda K H 0.320 0.137 0.381 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: 173 Number of extensions: 11 Number of successful extensions: 4 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: 233 Length of database: 232 Length adjustment: 23 Effective length of query: 210 Effective length of database: 209 Effective search space: 43890 Effective search space used: 43890 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 (21.8 bits) S2: 46 (22.3 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