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_011372955.1 SUDEN_RS06930 DUF1646 domain-containing protein
Query= TCDB::Q65NC0 (546 letters) >NCBI__GCF_000012965.1:WP_011372955.1 Length = 447 Score = 244 bits (624), Expect = 4e-69 Identities = 152/458 (33%), Positives = 238/458 (51%), Gaps = 40/458 (8%) Query: 68 FFAVLLFFFPEGLSYEGRMVLATTLWVAVWWITEAVPIPAASLLPIVLLPLTGALEGAAV 127 F LL F P L+ ++L ++ V W EA+P+ SLLPIVL P G L Sbjct: 18 FIVFLLSFIPFNLTQA--VLLGVIAFLVVLWTNEALPLGVVSLLPIVLFPSFGILSTNLT 75 Query: 128 TSSYGDPIVFLFLGGFLIALAMERWNLHKRIALNIISVVGTSTSRIVLGFMAATGFLSMW 187 T +Y +PI+FLFLGGF IA+A+E+ NLH+ IA + S+ + ++ A+G LS Sbjct: 76 TQNYANPIIFLFLGGFFIAIAVEKSNLHRWIAQKMFSIFPATARGVIFSLTIASGVLSSL 135 Query: 188 VSNTAAVMMMLPIGTAIIHQVSAVIKSERKDLAAEEAKFSKALIFSIGYAGTIGGLGTLI 247 +SNT ++++PI + ++EAK + Y ++GG+ T I Sbjct: 136 LSNTTTALLLIPIALFL----------------SDEAKLKMRFALGVAYGASVGGILTPI 179 Query: 248 GTPPNIILAANIKKLYGVEVSFGGWMAFAVPVVVILLVAVWLYLTKVAHPIKMKELPGGK 307 GTPPN+IL ++ SF WM P+VVI+L+ V L+ K+ Sbjct: 180 GTPPNLILLGFMQDKGMEAFSFVEWMWMMAPLVVIMLIVVSYLLSIGCSDAKIS------ 233 Query: 308 ELILEEKRKLGKMSFEETMVLLVFGFAAFMWVTRTFL---WDDKIPGIDDTMIAIFAASL 364 E+K+ L K ++ +LL+ G + + L W G+++++I + L Sbjct: 234 --FKEDKKTLNK---DQKKILLLLGGVVMLLLLNAPLGSHWSGL--GLNESVILLGGGLL 286 Query: 365 LFLIPSLNKGGRVLDWSVSKD-LPWGILLLFGGGLALATGFKETGLAEWIGGRLTVLDGF 423 LF P +LDW K +P+ I+ LFG G ++AT F T LA + L L F Sbjct: 287 LFAPPF-----SILDWMDDKGKVPFRIMFLFGAGFSIATAFSATSLASELASYLIALSDF 341 Query: 424 NFVVIVIISTALVLFLTEITSNTATATMILPVLASLALALNVHPYALMVPAAMAANCAFM 483 + +++ LV F TEITSNTA +++LP++ +LA+ N+ M+ A + A+ AFM Sbjct: 342 PTLFVLLCIAILVTFTTEITSNTALISVMLPIIYALAIQTNMDAKLFMMVATVCASYAFM 401 Query: 484 LPVGTPPNAIIFASGKLKISEMVRTGFVINIFTLILIV 521 LP+ TPPNAI +SG L + +M+R GF++N+ + +V Sbjct: 402 LPIATPPNAIAMSSGALNVKDMLRYGFLLNLIGVFFVV 439 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: 625 Number of extensions: 37 Number of successful extensions: 7 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: 447 Length adjustment: 34 Effective length of query: 512 Effective length of database: 413 Effective search space: 211456 Effective search space used: 211456 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