Align TreV, component of Trehalose porter (characterized)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Phaeo:GFF262 Length = 348 Score = 240 bits (612), Expect = 4e-68 Identities = 134/301 (44%), Positives = 191/301 (63%), Gaps = 20/301 (6%) Query: 3 VELIDIVKKYGKNI-VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIA 61 V L + K Y + + + KIE GEF V++GPSG GKSTLL+++AG+E + +G + Sbjct: 4 VTLNSVRKVYPNGVEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEGTLEI 63 Query: 62 DGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLG 121 + + P R++AMVFQNYALYP+M+VR NIA+ LK R + EI ++V +AAK+L Sbjct: 64 GDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQKVAEAAKMLN 123 Query: 122 ISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKE 181 + E LD+K +Q+SGGQ+QRVA+ RAIVR+P+ FL DEPLSNLDA++R R E+K +Q+ Sbjct: 124 LEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKALQRR 183 Query: 182 LKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFL 241 L T IYVTHDQ EA+++ADRI +L+ G+ EQ+ P +Y P + +VA F+G PMN L Sbjct: 184 LGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPPMNLL 243 Query: 242 PGELMK------------------EKAQEIGFRPEWVE-VGKGNLSCMVESVEASGESRY 282 + + A ++G RPE V+ V +G L+ VE +E G R Sbjct: 244 DATIANGQVTLPDGVSMGALDTSAQGAVKLGIRPEDVQLVAEGGLAIDVELIEELGAHRL 303 Query: 283 L 283 L Sbjct: 304 L 304 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: 262 Number of extensions: 6 Number of successful extensions: 1 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: 348 Length adjustment: 28 Effective length of query: 296 Effective length of database: 320 Effective search space: 94720 Effective search space used: 94720 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: 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