Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate WP_054558634.1 I595_RS06915 dicarboxylate/amino acid:cation symporter
Query= TCDB::Q01857 (444 letters) >NCBI__GCF_001306415.1:WP_054558634.1 Length = 437 Score = 206 bits (523), Expect = 2e-57 Identities = 131/415 (31%), Positives = 223/415 (53%), Gaps = 23/415 (5%) Query: 22 LYVQVLVAIAAGILLGHFYPEL--GTQ-----LKPLGDAFIKLVKMIIAPVIFLTVATGI 74 L+ Q+L+ + AG+L G +L G Q ++PLG F+KL+K+I P+I ++ G+ Sbjct: 6 LHWQILIGMIAGVLFGFAMNQLDWGEQFVADWIRPLGTIFVKLLKLIAIPLILASLVKGV 65 Query: 75 AGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASL------DPA 128 + + D+ K + + M ++ + +A+ IGL++ NV+QPG + D S + Sbjct: 66 SDLKDISKFRSIGLRTMAIYMGTTLVAITIGLVLVNVIQPGVAIPADTISKLVDTYSGDS 125 Query: 129 AVATFAAKAHEQSIVG---FLTNIIPTTIVGAFADGDI-LQVLFFSVLFGIALAMVGEK- 183 V + A+A Q G FL ++P V A +D + LQV+FF++ GI++ +VG+K Sbjct: 126 GVTSKLAEASMQKERGPLQFLEEMVPDNAVYAMSDNSLMLQVIFFTIFLGISMLLVGQKR 185 Query: 184 GEQVVNFLNSLTAPVFKLVAILMKAAPIGAFGAMA-FTIGKYGVGSIANLAMLIGTFYIT 242 + + F NSL V K+V ++M AP+ F +A + + L G + Sbjct: 186 AKPLKKFFNSLNDVVLKMVDLIMLTAPVAVFALLASVVVSSSDPDLLLALLKYAGVVLLG 245 Query: 243 SLLFVFIVLGAVARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMNKMEK-AGCKRS 301 LL V ++ + G+ + L I LL TSSS A LP M ++E+ G Sbjct: 246 LLLMVLFYCVIISFFTGYHPLKFLIKISPAQLLAFSTSSSAATLPVTMERVEEHIGVDAE 305 Query: 302 VVGLVIPTGYSFNLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITG 361 V V+P G + N+DGT++Y +AA+FI+QA L++ DQ+ ++ A+L+S G+A + G Sbjct: 306 VSSFVLPVGATVNMDGTSLYQGVAAVFISQALAFDLTFPDQLTIVFTALLASIGSAAVPG 365 Query: 362 AGFITLAATLSVV--PSVPVA-GMALILGIDRFMSECRALTNLVGNAVATIVVAR 413 AG + L L + P+ +A G+ALI +DR + CR + N+ G+++ I+VA+ Sbjct: 366 AGMVMLVIVLEAIGFPADKLAIGLALIFAVDRPLDMCRTVVNVTGDSMVAILVAK 420 Lambda K H 0.324 0.139 0.393 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: 473 Number of extensions: 28 Number of successful extensions: 7 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: 444 Length of database: 437 Length adjustment: 32 Effective length of query: 412 Effective length of database: 405 Effective search space: 166860 Effective search space used: 166860 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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