Align TRAP-type periplasmic solute-binding protein (characterized, see rationale)
to candidate 3607546 Dshi_0958 TRAP dicarboxylate transporter, DctP subunit (RefSeq)
Query= uniprot:Q930R1 (334 letters) >FitnessBrowser__Dino:3607546 Length = 326 Score = 160 bits (406), Expect = 3e-44 Identities = 89/260 (34%), Positives = 142/260 (54%), Gaps = 12/260 (4%) Query: 4 LLLATTAIAFGLSAAAPAFAEFNDRNIRVSNGINEDHPVGNGIKAMQACLDQKSGGKLKL 63 L+ A +A+ +AAA A + N + + E ++ + L+ + G++ + Sbjct: 8 LIAAASAMLMPAAAAAEAVMQIN-------SSLPEGSFAHVFLQEYEQRLEAAAPGEIDV 60 Query: 64 TAFWGGALGGDLQATQALRSGVQEAVVTSSSPLVGIIPALGVFDLPFLFANAQEAYTVLD 123 F LG + Q L G +A + S+S + + +FDLP+LF + T +D Sbjct: 61 QIFMSNTLGKEEDVLQGLGFGTHQASL-SASAVAQVNNRTSIFDLPYLFEDRAAVQTFID 119 Query: 124 GDFGDMMNEKLEAAGLVNLAYWENGFRNLSNSVRPVTKWEDFEGMKVRVMQNNIFLDTFQ 183 G+M+ + + G+V A W+NGFR ++N+VRP+ D +G+K+R N ++ F Sbjct: 120 SPAGEMLADGFDVTGMVLAAMWDNGFRQITNNVRPIVTPADLDGLKIRTPTNRQRVEMFN 179 Query: 184 NLGANATPMAFGEVFSALETKAIDAQENPYVTIDTSKFFEVQKYVTETNHAYTPFLFLFS 243 LGANATP++FGEV+SAL+ ID QENP ++T+K FEVQ Y++ TNH Y P F+ Sbjct: 180 TLGANATPLSFGEVYSALDQGTIDGQENPANVVETAKLFEVQGYMSLTNHVYLPTFFVIG 239 Query: 244 KPIFDSYTPEEQAALRECAV 263 +P +S TPE LRE + Sbjct: 240 EPFLNSLTPE----LRETVI 255 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: 247 Number of extensions: 11 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: 334 Length of database: 326 Length adjustment: 28 Effective length of query: 306 Effective length of database: 298 Effective search space: 91188 Effective search space used: 91188 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