Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate WP_035131390.1 Q763_RS03785 cation:dicarboxylase symporter family transporter
Query= TCDB::Q01857 (444 letters) >NCBI__GCF_000769915.1:WP_035131390.1 Length = 470 Score = 296 bits (758), Expect = 9e-85 Identities = 163/395 (41%), Positives = 241/395 (61%), Gaps = 8/395 (2%) Query: 26 VLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFLTVATGIAGMSDLQKVGR 85 +LV + G +GH +PE G L+ L F+KL+K I+ P+IF T+ GIAG S++++VGR Sbjct: 61 ILVCLVIGAAIGHEWPEAGQGLQVLSKIFLKLIKTIVGPLIFATLVYGIAGHSNIKQVGR 120 Query: 86 VAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVATFAAKAHEQSIVGF 145 + K++LYF +TLAL IGL N+ + G G+ + P + A Q+ Sbjct: 121 MGWKSLLYFEIVTTLALFIGLAAINITKAGEGI------IQPTDIKETIQAAEPQTWQQI 174 Query: 146 LTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQV-VNFLNSLTAPVFKLVAI 204 + +I P I + A+G++LQ++ FSV+FGIAL MV EK +V V+F SL+ +FK I Sbjct: 175 ILHIFPENIAKSMAEGEVLQIVVFSVIFGIALIMVPEKKRKVMVDFTQSLSEVMFKFTNI 234 Query: 205 LMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYITSLLFVFIVLGAVARYNGFSIVA 264 +M APIG AMA+T+G G+ + L L+ T Y L+FV IV +A + + A Sbjct: 235 VMYFAPIGVGAAMAYTVGHMGLSVLIPLLKLLLTLYGALLVFVIIVFIPIALFIKLDLRA 294 Query: 265 LLRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYSFNLDGTNIYMTL 324 ++ I E + + T+SSEAALP M ME G R +V V+P GYSFNLDGT +Y++L Sbjct: 295 FIKAIGEPVSIAFATTSSEAALPRAMEAMESIGVPRKIVSFVMPMGYSFNLDGTTLYLSL 354 Query: 325 AALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITGAGFITLAATLSVVPSVPVAGMAL 384 A++F+AQA GI LS G+Q++++ M++SKG AGI A + L T + ++PV + + Sbjct: 355 ASVFVAQAAGIDLSIGEQLIMVFTLMVTSKGVAGIPRASLVILMGTAASF-NLPVWPIFI 413 Query: 385 ILGIDRFMSECRALTNLVGNAVATIVVARWENELD 419 ILGID M R N+VGN +A+ V+A+WE E D Sbjct: 414 ILGIDELMDMARTSINVVGNCLASAVIAKWEGEFD 448 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: 483 Number of extensions: 22 Number of successful extensions: 4 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: 470 Length adjustment: 33 Effective length of query: 411 Effective length of database: 437 Effective search space: 179607 Effective search space used: 179607 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