Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), small permease component (characterized)
to candidate 7024208 Shewana3_1415 tripartite ATP-independent periplasmic transporter DctQ (RefSeq)
Query= reanno::PV4:5208944 (212 letters) >FitnessBrowser__ANA3:7024208 Length = 214 Score = 311 bits (796), Expect = 7e-90 Identities = 147/212 (69%), Positives = 174/212 (82%) Query: 1 MMSRFFSHIEEVVLNALITAMTLLVFVEVIARFFFNTGFLWIQELTLTICGWFVLFGMSY 60 M+SR F + EE VLN LIT MTLLVF EV+ARFFFNTGFLWIQELTLT+CGWFVLFGMSY Sbjct: 1 MISRIFGYFEEGVLNLLITLMTLLVFTEVVARFFFNTGFLWIQELTLTLCGWFVLFGMSY 60 Query: 61 GVKVGAHIGVDAFVKKLPAQGRKYTAILAVAICLIYCGMFLVGSWDYLAKMYQIGVPMED 120 GVKVGAHIGVDAFVK LP + +K T+++ ICL YCG+FL GSW+YL++MYQIGVPMED Sbjct: 61 GVKVGAHIGVDAFVKNLPPKAKKITSLVTALICLAYCGLFLKGSWEYLSQMYQIGVPMED 120 Query: 121 IDLPHFLIGGLDGDFAWEYLRIDVEEPAVPLWTSQSILLIGFILLTWRFLQLALAIITNK 180 I P FL+ LD DFAW L+IDVE+ AVP+W SQSILLIGF +LTWRFL+L +AI+ N+ Sbjct: 121 IHFPKFLLNSLDPDFAWNTLKIDVEDGAVPIWLSQSILLIGFSMLTWRFLELFIAILRNQ 180 Query: 181 TDGFAFADEAKESMHLIDQEAQADDKQPGDKK 212 GF FADEAKESMHLID+ AQ ++ +K+ Sbjct: 181 VSGFQFADEAKESMHLIDEAAQHAQQETDNKE 212 Lambda K H 0.329 0.144 0.453 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: 234 Number of extensions: 8 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: 212 Length of database: 214 Length adjustment: 22 Effective length of query: 190 Effective length of database: 192 Effective search space: 36480 Effective search space used: 36480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 45 (21.9 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