Align TRAP-type periplasmic solute-binding protein (characterized, see rationale)
to candidate 3609944 Dshi_3326 TRAP dicarboxylate transporter, DctP subunit (RefSeq)
Query= uniprot:Q930R1 (334 letters) >FitnessBrowser__Dino:3609944 Length = 325 Score = 167 bits (423), Expect = 3e-46 Identities = 96/287 (33%), Positives = 153/287 (53%), Gaps = 7/287 (2%) Query: 46 IKAMQACLDQKSGGKLKLTAFWGGALGGDLQATQALRSGVQEAVVTSSSPLVGIIPALGV 105 + A C + K G ++ F LG D + Q L+ G Q + SS + + P G+ Sbjct: 42 VNAFAECANGKLGDAAEVQTFGASQLGNDREMLQKLKLG-QVHMSLPSSVMSSVAPEFGI 100 Query: 106 FDLPFLFANAQEAYTVLDGDFGDMMNEKLEAAGLVNLAYWENGFRNLSNSVRPVTKWEDF 165 F++P++ + + V + GD E G + Y ENGFR+++N+VRP+ ED Sbjct: 101 FEMPYIIRDREHMKRV-QAELGDTFQEAALGQGYRIIGYMENGFRHITNNVRPINTPEDL 159 Query: 166 EGMKVRVMQNNIFLDTFQNLGANATPMAFGEVFSALETKAIDAQENPYVTIDTSKFFEVQ 225 G+K+R + FQ GAN TPM+F EVF+AL+TK ID QENPY I ++KF EVQ Sbjct: 160 AGVKLRTPNGEWRVKMFQEYGANPTPMSFSEVFTALQTKVIDGQENPYAQIASAKFQEVQ 219 Query: 226 KYVTETNHAYTPFLFLFSKPIFDSYTPEEQAALRECAVVGRDEERKVIQDLNKKSLEKIK 285 Y++ T H YTP L ++ + S+ + +AAL C +D ++ +L + L+ IK Sbjct: 220 SYLSITGHVYTPAYVLVAENQWQSWPEDVRAALESCGTETQDTVYEIAANLETELLDVIK 279 Query: 286 EAGLEVNTLSAEEQARIREKSMVVYEKHKAEI--GAEVVDAILAKLE 330 AG+EVN ++A S +Y+ A++ AE+++ + + E Sbjct: 280 AAGVEVN---EADKAAFVAASTPIYDAFAAQVEGAAEMIETVQSLAE 323 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: 231 Number of extensions: 7 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: 325 Length adjustment: 28 Effective length of query: 306 Effective length of database: 297 Effective search space: 90882 Effective search space used: 90882 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