Align TRAP-type periplasmic solute-binding protein (characterized, see rationale)
to candidate SM_b21353 SM_b21353 periplasmic C4-dicarboxylate transport protein
Query= uniprot:Q930R1 (334 letters) >FitnessBrowser__Smeli:SM_b21353 Length = 325 Score = 175 bits (443), Expect = 2e-48 Identities = 102/302 (33%), Positives = 165/302 (54%), Gaps = 10/302 (3%) Query: 30 IRVSNGINEDHPVGNGIKAMQACLDQKSGGKLKLTAFWGGALGGDLQATQALRSGVQEAV 89 +R S+ + +P G+K + +++ G+ + + LG + + +RSGV E Sbjct: 28 LRSSDTHPDGYPTVEGVKYFGELVKERTAGRYSVEVYHSAQLGEEKDTIEQVRSGVIELN 87 Query: 90 VTSSSPLVGIIPALGVFDLPFLFANAQEAYTVLDGDFGDMMNEKLEAAGLVNLAYWENGF 149 S +P G + V LP+LF + + + V+DG GD + + E AG+V LA+++ G Sbjct: 88 RVSMAPFNGTVKESIVPALPYLFRSEEHMHKVMDGAIGDQIKKAFEGAGVVVLAFYDAGA 147 Query: 150 RNLSNSVRPVTKWEDFEGMKVRVMQNNIFLDTFQNLGANATPMAFGEVFSALETKAIDAQ 209 R+ N +P+ ED +G+K RV+Q++IF+D LGANATPM +GEV+S +ET ID Sbjct: 148 RSFYNKQKPINTVEDMKGLKFRVIQSDIFVDMVAALGANATPMPYGEVYSGIETGVIDGA 207 Query: 210 ENPYVTIDTSKFFEVQKYVTETNHAYTPFLFLFSKPIFDSYTPEEQAALRECAVVGRDEE 269 EN + + DT+K FEV K + H P +F+ +K FD TPE+Q ++ A ++ Sbjct: 208 ENNFPSYDTAKHFEVAKNYSLDEHTILPEVFVMNKAAFDKLTPEDQEIFKQAAKDSVAKQ 267 Query: 270 RKVIQDLNKKSLEKIKEAGLEVNTLSAEEQARIREKSMVVYEKHKAEIGAEVVDAILAKL 329 R++ K+S K++ AG ++ T E+Q I + VYEKH V D +L K+ Sbjct: 268 RELWAAKVKESRAKVEAAGAKITT--PEKQGFI-DAMKPVYEKH-------VTDEVLKKM 317 Query: 330 EE 331 E Sbjct: 318 VE 319 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: 244 Number of extensions: 9 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: 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