Align TreV, component of Trehalose porter (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 135 bits (341), Expect = 1e-36 Identities = 83/253 (32%), Positives = 135/253 (53%), Gaps = 10/253 (3%) Query: 3 VELIDIVKKY---GKNI-VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGK 58 + +D+ K Y GK+I + + I GE F I+G SG GKSTL++++ +E+ G Sbjct: 2 IRFVDVHKSYRVDGKDIPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGS 61 Query: 59 IIADGADITDKPP-----EKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKE-EIIER 112 I+ DG ++T ++R + M+FQ++ L + +V DNIAFPL++ G +I R Sbjct: 62 ILIDGTEMTALGDAALRAQRRRIGMIFQHFNLLSSQTVADNIAFPLRLAGETDAGKIKAR 121 Query: 113 VEKAAKLLGISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTAR 172 V++ + +G+ K Q+SGGQ+QRV +ARA+ PS L DE S LD + + Sbjct: 122 VDELLRRVGLEAHASKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASVL 181 Query: 173 GELKRIQKELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQF 232 L I +ELK T + +TH+ + DR+A+L G+ + ++ +P+ +F Sbjct: 182 ELLAEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTRRF 241 Query: 233 VGEFPMNFLPGEL 245 V E GEL Sbjct: 242 VNEALPEEAAGEL 254 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: 242 Number of extensions: 13 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: 336 Length adjustment: 28 Effective length of query: 296 Effective length of database: 308 Effective search space: 91168 Effective search space used: 91168 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