Align TreV, component of Trehalose porter (characterized)
to candidate PP_1722 PP_1722 ABC transporter, ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Putida:PP_1722 Length = 329 Score = 216 bits (549), Expect = 8e-61 Identities = 120/277 (43%), Positives = 174/277 (62%), Gaps = 8/277 (2%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 V + + K Y + V I IE GEF +LGPSG GKSTLL+ +AG+ +D G+I+ D Sbjct: 4 VSVQKLQKSYAGSPVFERIDCHIERGEFVTLLGPSGCGKSTLLRCIAGLTSVDSGQILLD 63 Query: 63 GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122 G DI P+KR + MVFQ+YAL+PNM+V N+AF L+M+ +K +E RV + +L+ + Sbjct: 64 GHDIVPLSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVKADESQLRVREVLELVEL 123 Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182 + + Q+SGGQ QRVALAR++V P LLDEPLS LDAR+R R +++ IQ+EL Sbjct: 124 GKFAGRYPHQLSGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKHLREQIRAIQREL 183 Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242 T I+VTHDQ+EAL+++DRI ++++G+ Q D +TLY P + A F+G + N L Sbjct: 184 GLTTIFVTHDQEEALTMSDRIFLMNQGRIVQSGDAETLYTAPVDLFAAGFIGNY--NLLD 241 Query: 243 GE-----LMKEKAQEIGFRPEWVEVGK-GNLSCMVES 273 + L + A + RPE + +G+ G L V S Sbjct: 242 ADSASRLLQRPVASRLAIRPESITLGEHGELDAEVRS 278 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: 235 Number of extensions: 5 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: 329 Length adjustment: 28 Effective length of query: 296 Effective length of database: 301 Effective search space: 89096 Effective search space used: 89096 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