Align TRAP dicarboxylate transporter, DctP subunit (characterized, see rationale)
to candidate 3607546 Dshi_0958 TRAP dicarboxylate transporter, DctP subunit (RefSeq)
Query= uniprot:Q88NN8 (323 letters) >FitnessBrowser__Dino:3607546 Length = 326 Score = 125 bits (313), Expect = 2e-33 Identities = 92/306 (30%), Positives = 148/306 (48%), Gaps = 13/306 (4%) Query: 9 LAVLPFAFSVAMPASALDIKFAEIH---PAGYPTVVAEQNMGKKLEDASNGEITFKMFAG 65 LA++ A ++ MPA+A +I+ P G V Q ++LE A+ GEI ++F Sbjct: 6 LALIAAASAMLMPAAAAAEAVMQINSSLPEGSFAHVFLQEYEQRLEAAAPGEIDVQIFMS 65 Query: 66 GVLGSEKEVIEQAQIGAVQMTRVSLGIVGPVVPDVNVFNMPFVFRDHDHMRKIIDGEIGQ 125 LG E++V++ G Q + +S V V ++F++P++F D ++ ID G+ Sbjct: 66 NTLGKEEDVLQGLGFGTHQAS-LSASAVAQVNNRTSIFDLPYLFEDRAAVQTFIDSPAGE 124 Query: 126 EILDKITNSDFNLVALAWMDGGSRSIYTKKPVRSLEDLKGMKIRVQGNPLFIDMMNAMGG 185 + D + L A+ W +G + +P+ + DL G+KIR N ++M N +G Sbjct: 125 MLADGFDVTGMVLAAM-WDNGFRQITNNVRPIVTPADLDGLKIRTPTNRQRVEMFNTLGA 183 Query: 186 NGIAMDTGEIFSALQTGVIDGAENNPPTLLEHNHFQSAKYYTLTGHLILPEPVVMSKTTW 245 N + GE++SAL G IDG EN + F+ Y +LT H+ LP V+ + Sbjct: 184 NATPLSFGEVYSALDQGTIDGQENPANVVETAKLFEVQGYMSLTNHVYLPTFFVIGEPFL 243 Query: 246 NKLSPEQQALVKKVAREAQMEERALWDAKS-----AASEEKLKAAGVEFITVDK--KPFY 298 N L+PE + V VA+E W KS AA +EKL+ ++F P Y Sbjct: 244 NSLTPELRETVISVAKEVGPWSFE-WGEKSDTETIAALQEKLEVNEIDFAAFQSAAAPLY 302 Query: 299 DATASV 304 D+ V Sbjct: 303 DSPTFV 308 Lambda K H 0.318 0.134 0.381 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: 193 Number of extensions: 9 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 323 Length of database: 326 Length adjustment: 28 Effective length of query: 295 Effective length of database: 298 Effective search space: 87910 Effective search space used: 87910 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