Align The Na+-coupled dicarboxylate (succinate; malate; fumarate) transporter, SdcL (transports aspartate, α-ketoglutarate and oxaloacetate with low affinity). Km for succinate, ~6 (characterized)
to candidate WP_005808163.1 DHAF_RS01040 sodium:proton antiporter
Query= TCDB::Q65NC0 (546 letters) >NCBI__GCF_000021925.1:WP_005808163.1 Length = 498 Score = 209 bits (533), Expect = 2e-58 Identities = 137/452 (30%), Positives = 233/452 (51%), Gaps = 24/452 (5%) Query: 80 LSYEGRMVLATTLWVAVWWITEAVPIPAASLLPIVLLPLTGALEGAA-VTSSYGDPIVFL 138 L++EG+ V A ++ + W+TEA+P P +L I++L L G A V + G ++F Sbjct: 51 LTFEGKAVFAVLVYAVILWLTEAIPFPITALSMIIILHLMGVSTFTALVKTGLGSSVLFF 110 Query: 139 FLGGFLIALAMERWNLHKRIALNIISVVGTSTSRIVLGFMAATGFLSMWVSNTAAVMMML 198 +G ++ A+ L RI L ++S VGT T RIV FMA FLSMWV++ A M+L Sbjct: 111 LMGAMGLSAAITVSGLANRIMLGVLSKVGTRTDRIVFTFMALGTFLSMWVTDMAVAAMLL 170 Query: 199 PIGTAIIHQVSAVIKSERKDLAAEEAKFSKALIFSIGYAGTIGGLGTLIGTPPNIILAAN 258 P+G I+ Q S K L ++ F + L+ I Y IGG T G NI+ + Sbjct: 171 PLGVNILRQ------SGCKPL---QSNFGRCLMIGIVYGALIGGTSTPAGCGANILAISY 221 Query: 259 IKKLYGVEVSFGGWMAFAVPVVVILLVAVWLYLTKVAHPIKMKELPGGKELILEEKRKLG 318 +++L + SF WM VP +++L A W L KV P +++ +P + + + ++LG Sbjct: 222 LRELTEADASFLQWMIVGVPGALMMLPAGWFLLMKV-FPPEIRNVPIELDDVRRQNKELG 280 Query: 319 KMSFEETMVLLVFGFAAFMWVTRTFLWDDKIPGIDDTMIAIFAASLLFLIPSLNKGGRVL 378 ++ +E +VF A MW+ + I + A+FA LLFL P L G Sbjct: 281 PLTRQERNTTIVFFTAVTMWLGAPLIKSLTGISIPEDFTALFAFLLLFL-PGLQVFG--- 336 Query: 379 DW-SVSKDLPWGILLLFGGGLALATGFKETGLAEWIG-GRLTVLDGFN----FVVIVIIS 432 W ++ + W L+L GG+A ETG A +I G L + + ++++ Sbjct: 337 SWKEANEHIDWSGLMLIAGGIAAGMLLAETGTARYIAWGALNGIGALHPMLRVAAVLVLV 396 Query: 433 TALVLFLTEITSNTATATMILPVLASLALALNVHPYALMVPAAMAANCAFMLPVGTPPNA 492 AL +F +SN+ T +++P++ +LAL L ++P+ + PA +A + AF++ +P N Sbjct: 397 EALKIF---FSSNSVTGAVVIPLVIALALDLGMNPWIVAGPAGIATSMAFIMVTSSPTNV 453 Query: 493 IIFASGKLKISEMVRTGFVINIFTLILIVGAV 524 I ++SG I + + G ++ + ++ + +V Sbjct: 454 IPYSSGYFSIKDFAKCGVLMTVIGIVAVTLSV 485 Lambda K H 0.326 0.140 0.425 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: 653 Number of extensions: 36 Number of successful extensions: 9 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: 546 Length of database: 498 Length adjustment: 35 Effective length of query: 511 Effective length of database: 463 Effective search space: 236593 Effective search space used: 236593 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: 52 (24.6 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