Align TreV, component of Trehalose porter (characterized)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Pedo557:CA265_RS15880 Length = 330 Score = 143 bits (360), Expect = 7e-39 Identities = 86/252 (34%), Positives = 140/252 (55%), Gaps = 9/252 (3%) Query: 18 INGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDKP----PEK 73 I ++ +I+ G+ I+G SG GKSTLLK + G+ K D+G+I + + P Sbjct: 23 IKNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDEGEIFFEDKRVKGPDEQLIPGH 82 Query: 74 RNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKVTQI 133 + + MV Q+++L V DNIA L +K + E+ + + L I + +KK+ ++ Sbjct: 83 KQMKMVTQDFSLNIYAKVYDNIASQLSNTDLKTKA--EKTLQIMEHLRILPLQNKKIIEL 140 Query: 134 SGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVTHDQ 193 SGG+QQRVA+A+A+V + LLDEP S +DA ++ R ++KR+ E T I V+HD Sbjct: 141 SGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKNQLRADIKRVASETGVTVILVSHDP 200 Query: 194 KEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGE-FPMNFLPGEL--MKEKA 250 + L LAD++ IL G+ Q P +Y++PK + AQ +G ++ E +K + Sbjct: 201 ADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIYTAQILGNAVVLSQADAEKIGLKTER 260 Query: 251 QEIGFRPEWVEV 262 + F PEW E+ Sbjct: 261 NSVVFYPEWAEI 272 Lambda K H 0.318 0.137 0.385 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: 269 Number of extensions: 12 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: 324 Length of database: 330 Length adjustment: 28 Effective length of query: 296 Effective length of database: 302 Effective search space: 89392 Effective search space used: 89392 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: 48 (23.1 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