Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate BWI76_RS08460 BWI76_RS08460 dicarboxylate/amino acid:cation symporter
Query= TCDB::Q01857 (444 letters) >FitnessBrowser__Koxy:BWI76_RS08460 Length = 435 Score = 275 bits (703), Expect = 2e-78 Identities = 147/364 (40%), Positives = 226/364 (62%), Gaps = 5/364 (1%) Query: 54 FIKLVKMIIAPVIFLTVATGIAGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQ 113 F+++VKMIIAP++ T+ GIA M D + +GR+ K F+ S L++ +GL++ N+ Q Sbjct: 47 FLRMVKMIIAPLVISTLVVGIAKMGDAKTLGRIFSKTFFLFICASLLSIALGLVIVNLFQ 106 Query: 114 PGAGMNIDPASLDPAAVATFAAKAHEQSIVGFLTNIIPTTIVGAFADGDILQVLFFSVLF 173 PGAG+N P D AVA A ++ ++ F+++ +PT+IV A A +ILQ++ FS+ Sbjct: 107 PGAGINFVPH--DAGAVA--AVQSEPFTLKVFISHAVPTSIVDAMARNEILQIVVFSIFL 162 Query: 174 GIALAMVGEKGEQVVNFLNSLTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLA 233 G +LA +GEK E +V L+SL + KL +M AP+ F A++ I + G+G + + Sbjct: 163 GCSLAAIGEKAEPIVKVLDSLVHVMLKLTGYVMLFAPLTVFAAISGLIAERGLGVMVSAG 222 Query: 234 MLIGTFYITSLLFVFIVLGAVARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMNKM 293 + +G FY+T + I++G G I L + I E LL TSSSEAA PG ++K+ Sbjct: 223 IFMGEFYLTLGMLWAILIGLSTVIVGPCISRLTKAIFEPALLAFTTSSSEAAFPGTLDKL 282 Query: 294 EKAGCKRSVVGLVIPTGYSFNLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSS 353 EK G + V+P GYSFNL G+ Y + A +FIAQA +HLS G+QI +LL+ ML+S Sbjct: 283 EKFGVSSKIASFVLPIGYSFNLVGSMAYCSFATVFIAQACNVHLSMGEQITMLLILMLTS 342 Query: 354 KGAAGITGAGFITLAATLSVVPSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVVAR 413 KG AG+ A + +AATL+ ++P AG+ L++G+D F+ R+ TN++ NA+ +V R Sbjct: 343 KGMAGVPRASMVVIAATLNQF-NIPEAGLILLMGVDPFLDMGRSATNVMSNAMGAAIVGR 401 Query: 414 WENE 417 WE E Sbjct: 402 WEGE 405 Score = 25.4 bits (54), Expect = 0.004 Identities = 48/210 (22%), Positives = 83/210 (39%), Gaps = 51/210 (24%) Query: 28 VAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFLTVATGIAGMSDLQKVGRVA 87 V ++AGI +G FY LG L I L +I+ P I S L K + Sbjct: 217 VMVSAGIFMGEFYLTLGM----LWAILIGLSTVIVGPCI-----------SRLTKA--IF 259 Query: 88 GKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVATFAAKAHEQSIVGFLT 147 A+L F T S+ A PG ++ + + +A+F +G+ Sbjct: 260 EPALLAFTTSSSEAAF----------PGTLDKLEKFGVS-SKIASFVLP------IGYSF 302 Query: 148 NIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQVVNFLNSLTAPVFKLVAILMK 207 N++ + +FA +F + + L+M GEQ+ L + L + M Sbjct: 303 NLVGSMAYCSFA------TVFIAQACNVHLSM----GEQITMLL------ILMLTSKGMA 346 Query: 208 AAPIGAFGAMAFTIGKYGVGSIANLAMLIG 237 P + +A T+ ++ + A L +L+G Sbjct: 347 GVPRASMVVIAATLNQFNIPE-AGLILLMG 375 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: 510 Number of extensions: 27 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 444 Length of database: 435 Length adjustment: 32 Effective length of query: 412 Effective length of database: 403 Effective search space: 166036 Effective search space used: 166036 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