Align TRAP-type periplasmic solute-binding protein (characterized, see rationale)
to candidate WP_092483299.1 BM299_RS09265 TRAP transporter substrate-binding protein
Query= uniprot:Q930R1 (334 letters) >NCBI__GCF_900115975.1:WP_092483299.1 Length = 343 Score = 236 bits (602), Expect = 6e-67 Identities = 111/297 (37%), Positives = 184/297 (61%), Gaps = 3/297 (1%) Query: 30 IRVSNGINEDHPVGNGIKAMQACLDQKSGGKLKLTAFWGGALGGDLQATQALRSGVQEAV 89 ++ + + E HP G++ + +++K+GG++++ + G +G + + L+ G + V Sbjct: 43 LKAGHAVAESHPYHLGLEKFKQIVEEKTGGQVQIDIYANGTIGSERDMIEGLQLGTIDLV 102 Query: 90 VTSSSPLVGIIPALGVFDLPFLFANAQEAYTVLDGDFGDMMNEKLEAAGLVNLAYWENGF 149 +TS+ P++ +P +GV DLPFLF++ + AY VLDG+ G + E+ G+V LA+WENGF Sbjct: 103 LTSTGPVINFVPEMGVVDLPFLFSSREHAYQVLDGEIGQDLLEQFGDIGIVGLAFWENGF 162 Query: 150 RNLSNSVRPVTKWEDFEGMKVRVMQNNIFLDTFQNLGANATPMAFGEVFSALETKAIDAQ 209 RNL+NS RP+ ED +G+K+R M+N + F+ LGA+ TPMA+GEV++AL+ K ID Q Sbjct: 163 RNLTNSERPINSVEDIQGLKIRTMENEVHQAAFKELGADPTPMAWGEVYTALQQKTIDGQ 222 Query: 210 ENPYVTIDTSKFFEVQKYVTETNHAYTPFLFLFSKPIFDSYTPEEQAALRECAVVGRDEE 269 ENP I K +EVQKY+ T H Y+P L L + D +PE+Q +++ AV E Sbjct: 223 ENPIPIIYNMKIYEVQKYLALTGHFYSPALLLIGQKSLDKLSPEQQNIIKKAAVEAATYE 282 Query: 270 RKVIQDLNKKSLEKIKEAGLEVNTLSAEEQARIREKSMVVYEKHKAEIGAEVVDAIL 326 R+ I+ + L K++E G+ ++ ++ +RE +M VYEK++ G + + IL Sbjct: 283 REQIKVQEDEQLAKLEEKGM---VITRPDKNALREATMAVYEKYEGRFGKDTIQKIL 336 Lambda K H 0.317 0.133 0.374 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: 297 Number of extensions: 12 Number of successful extensions: 2 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: 334 Length of database: 343 Length adjustment: 28 Effective length of query: 306 Effective length of database: 315 Effective search space: 96390 Effective search space used: 96390 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 Apr 09 2024. 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