Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate WP_012385213.1 BIND_RS11330 dicarboxylate/amino acid:cation symporter
Query= TCDB::Q01857 (444 letters) >NCBI__GCF_000019845.1:WP_012385213.1 Length = 443 Score = 473 bits (1217), Expect = e-138 Identities = 242/428 (56%), Positives = 320/428 (74%), Gaps = 11/428 (2%) Query: 2 IAAPLDAVAGSKGKKPFYSHLYVQVLVAIAAGILLGHFYPELGTQ--LKPLGDAFIKLVK 59 +A PL G+ PFY LYVQVL+ I G+L G +P + +K LGD FIKL+K Sbjct: 9 LAKPL----GAPRAVPFYRILYVQVLIGILLGVLFGWLWPATASADWVKALGDGFIKLIK 64 Query: 60 MIIAPVIFLTVATGIAGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMN 119 M+IAP+IF TV +GIA +S QKVGR+ KA++YF ST AL++GL++ N+VQPG G+ Sbjct: 65 MMIAPIIFCTVVSGIAHVSSAQKVGRIGVKALVYFEVVSTFALVLGLVIGNLVQPGRGI- 123 Query: 120 IDPASLDPAAVATFAAKAHEQSIVGFLTNIIPTTIVGAFADGDILQVLFFSVLFGIALAM 179 +D AVA + + H S V FL ++IP ++VG FA GD+LQVL FS+LFG AL Sbjct: 124 --ADKVDAGAVAKYVGQEH--STVQFLLDLIPDSVVGGFARGDVLQVLLFSILFGFALLG 179 Query: 180 VGEKGEQVVNFLNSLTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTF 239 +G +GE + ++ + VF ++AI+M+AAPIGAFGAMA+T+G+YG ++ NL L+ TF Sbjct: 180 LGSRGESLTKLIDDVAQAVFGVIAIVMRAAPIGAFGAMAYTVGRYGPQTLGNLLGLVATF 239 Query: 240 YITSLLFVFIVLGAVARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCK 299 Y+T++LF+ IVLG +AR GFSI L YIK+ELL+VLGTSSSE+ALP LM K+E+ GC Sbjct: 240 YLTAILFIVIVLGTIARLAGFSIFKFLAYIKDELLIVLGTSSSESALPALMEKLERLGCS 299 Query: 300 RSVVGLVIPTGYSFNLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGI 359 + VVGLV+PTGYSFNLDGTNIYMTLA LF+AQA G+ L+ +QI +LLVAM++SKGA+GI Sbjct: 300 KPVVGLVVPTGYSFNLDGTNIYMTLATLFVAQALGVPLNLEEQITILLVAMVASKGASGI 359 Query: 360 TGAGFITLAATLSVVPSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVVARWENELD 419 +GAGFITLAATL+ V + V GMA++LG+D+FMSECRALTN++GN VATI+V+RWE E+D Sbjct: 360 SGAGFITLAATLAAVNPILVPGMAMLLGVDKFMSECRALTNIIGNGVATIIVSRWEKEID 419 Query: 420 TVQLAAAL 427 L AAL Sbjct: 420 PRALRAAL 427 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: 636 Number of extensions: 37 Number of successful extensions: 3 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: 443 Length adjustment: 32 Effective length of query: 412 Effective length of database: 411 Effective search space: 169332 Effective search space used: 169332 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