Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate Ac3H11_719 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate, aspartate
Query= TCDB::Q01857 (444 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_719 Length = 456 Score = 588 bits (1516), Expect = e-172 Identities = 302/431 (70%), Positives = 353/431 (81%), Gaps = 3/431 (0%) Query: 17 PFYSHLYVQVLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFLTVATGIAG 76 PFY LY QV++AI G+LLGHF P G LKPLGDAFIKLVKMIIAPVIFLT+ TGIAG Sbjct: 15 PFYRQLYFQVVLAIVLGVLLGHFEPSYGEALKPLGDAFIKLVKMIIAPVIFLTIVTGIAG 74 Query: 77 MSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVATFAAK 136 MS L VGRV GKAM YFL FSTLAL++GL+VANVVQPGAGMNI+ A LD +AV + AK Sbjct: 75 MSQLSTVGRVFGKAMAYFLFFSTLALVVGLVVANVVQPGAGMNINVADLDQSAVKGYVAK 134 Query: 137 AHEQSIVGFLTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQVVNFLNSLTA 196 +HE ++ GF +IIP T+V F +ILQVL +VLFG+ LAMVG+ G V+NFL++LT Sbjct: 135 SHEMTLTGFALDIIPKTLVSPFVGDNILQVLLVAVLFGVGLAMVGDAGRPVLNFLDALTT 194 Query: 197 PVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYITSLLFVFIVLGAVAR 256 PVFK+V I+MKAAP+GAFGAMAFTIGK+G+GS+ NLA L+G+FYITSLLFV ++LG VAR Sbjct: 195 PVFKVVGIVMKAAPLGAFGAMAFTIGKFGLGSLVNLAWLVGSFYITSLLFVVVILGFVAR 254 Query: 257 YNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYSFNLD 316 GFS+ L RY+K EL+LVLGTSSSE+ALP LM KMEKAGC +SVVGLV+PTGYSFNLD Sbjct: 255 LCGFSVFKLCRYLKAELMLVLGTSSSESALPSLMEKMEKAGCSKSVVGLVVPTGYSFNLD 314 Query: 317 GTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITGAGFITLAATLSVVPS 376 GTNIYMTLAALFIAQAT L+ G Q+ LLLVAMLSSKGAAG+TGAGFITLAATL+VVP Sbjct: 315 GTNIYMTLAALFIAQATNTELTLGHQVALLLVAMLSSKGAAGVTGAGFITLAATLAVVPE 374 Query: 377 VPVAGMALILGIDRFMSECRALTNLVGNAVATIVVARWENELDTVQLAAALGGQ---TGE 433 VPVAGMALILG+DRFMSECR+LTN +GNAVAT+VV+RWEN LD +L AAL G Sbjct: 375 VPVAGMALILGVDRFMSECRSLTNFIGNAVATVVVSRWENALDHERLDAALNGHPLPAAV 434 Query: 434 DTSAAGLQPAE 444 +AA + PA+ Sbjct: 435 TAAAAPVVPAD 445 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: 716 Number of extensions: 35 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: 444 Length of database: 456 Length adjustment: 33 Effective length of query: 411 Effective length of database: 423 Effective search space: 173853 Effective search space used: 173853 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 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