Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate WP_085545458.1 B9Y55_RS11270 dicarboxylate/amino acid:cation symporter
Query= TCDB::Q01857 (444 letters) >NCBI__GCF_900177735.1:WP_085545458.1 Length = 400 Score = 238 bits (606), Expect = 3e-67 Identities = 141/411 (34%), Positives = 231/411 (56%), Gaps = 15/411 (3%) Query: 9 VAGSKGKKPFYSHLYVQVLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFL 68 ++ SK P + + ++ IAAG LG P++ ++P+G FI L+KM+I P++F Sbjct: 1 MSNSKKGVPLIWRITIGFVLGIAAGAFLG---PKVSI-VEPVGKVFITLLKMLIVPLVFS 56 Query: 69 TVATGIAGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPA 128 ++ G++ + + + +GR+ K +L +L + +A++IGL + + QPG+GM I+ Sbjct: 57 SLVVGVSSIGEPKTLGRIGVKTILIYLMTTAVAIVIGLGMGHFFQPGSGMAIEGVE---- 112 Query: 129 AVATFAAKAHEQSIVGFLTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQVV 188 A A AA A + I+G + P V A A G +LQ++ F++ FGIA + G+KG+ V+ Sbjct: 113 AAAGRAAPALSEVIIG----MFPDNPVQALAQGHMLQIIVFALFFGIAAMLAGDKGKPVI 168 Query: 189 NFLNSLTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYITSLLFVF 248 +F+ S+ ++K+ ++M AP G F +A T+ KYG+ +A A +IG Y+ ++ Sbjct: 169 SFMESMAETMYKVTDLVMNLAPYGVFALIAVTVSKYGLSVLAPFAKVIGAVYLGCIVHAI 228 Query: 249 IVL-GAVARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMN-KMEKAGCKRSVVGLV 306 +V G VA S + + I+E L T SS A LP M E G + V Sbjct: 229 VVYSGLVAVVTKKSPIWFFKGIQEASLTAFVTRSSSATLPVTMTCTQENMGISEKISSFV 288 Query: 307 IPTGYSFNLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITGAGFIT 366 +P G + N+DGT +Y + ALFIAQA GI LS G Q+ +++ A L+S G AG+ GAG I Sbjct: 289 LPLGATINMDGTALYQGVCALFIAQAFGIDLSIGAQVGIIVTATLASVGTAGVPGAGLIM 348 Query: 367 LAATLSVVPSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVVARWENE 417 L ++ +P+ G+A++ GID + R N+ G+A T V+A+ E E Sbjct: 349 LTLVVTQA-GLPMEGVAMVAGIDAVLDMARTSLNVTGDACVTAVIAKTEGE 398 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: 437 Number of extensions: 28 Number of successful extensions: 5 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: 400 Length adjustment: 32 Effective length of query: 412 Effective length of database: 368 Effective search space: 151616 Effective search space used: 151616 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: 50 (23.9 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