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 Echvi_4197 Echvi_4197 anion transporter
Query= TCDB::Q65NC0 (546 letters) >FitnessBrowser__Cola:Echvi_4197 Length = 491 Score = 500 bits (1287), Expect = e-146 Identities = 245/485 (50%), Positives = 343/485 (70%), Gaps = 8/485 (1%) Query: 57 QKIGLLLGPALFFAVLLFFFPEGLSYEGRMVLATTLWVAVWWITEAVPIPAASLLPIVLL 116 +K L+LGP +F ++L P G+S E VLA TLW+A+WWI EAVPI +LLPIVL Sbjct: 7 KKWSLILGPMVFIGLILLDPPSGMSEEALKVLAVTLWMAIWWIAEAVPIAVTALLPIVLF 66 Query: 117 PLTGALEGAAVTSSYGDPIVFLFLGGFLIALAMERWNLHKRIALNIISVVGTSTSRIVLG 176 P+TGA+E T +YG +FL++GGF++ALA+ERW LH+RIAL IIS++G++ + I+LG Sbjct: 67 PITGAVEIGITTEAYGHKYIFLYMGGFILALAIERWGLHQRIALIIISLIGSNMNSIMLG 126 Query: 177 FMAATGFLSMWVSNTAAVMMMLPIGTAIIHQVSAVIKSERKDLAAE--EAKFSKALIFSI 234 FM AT FLSMW+SNTA +MMLPIG AI++Q + V D+ + E + KAL+ +I Sbjct: 127 FMLATAFLSMWISNTATAVMMLPIGMAIVNQFAKV-----SDIYPDNREKEVGKALMLAI 181 Query: 235 GYAGTIGGLGTLIGTPPNIILAANIKKLYGVEVSFGGWMAFAVPVVVILLVAVWLYLTKV 294 Y+ +IGG TLIGTPPN++LA I++LY V++SF WM F P+ ++LL+ W YLT Sbjct: 182 AYSASIGGFATLIGTPPNLVLAGIIEELYDVKLSFLDWMKFGFPLSMLLLIICWKYLTTY 241 Query: 295 AHPIKMKELPGGKELILEEKRKLGKMSFEETMVLLVFGFAAFMWVTRTFLWDDKIPGIDD 354 A K + PGGK+ I + + LGK+SFEE VL++F A W+ R+F+ +PGIDD Sbjct: 242 AFDCKKVDFPGGKQEINKMLKALGKISFEEKWVLIIFALTAAAWILRSFI-QRLLPGIDD 300 Query: 355 TMIAIFAASLLFLIPSLNKGGRVLDWSVSKDLPWGILLLFGGGLALATGFKETGLAEWIG 414 +IA+ AA LF++PS + ++++W + LPWGI+LLFGGG+ALA GF TGLAEWI Sbjct: 301 AVIALMAAITLFVLPSKSGKRKLINWEEAVKLPWGIILLFGGGMALAKGFGITGLAEWIA 360 Query: 415 GRLTVLDGFNFVVIVIISTALVLFLTEITSNTATATMILPVLASLALALNVHPYALMVPA 474 G++ ++G + +++++I A+V FLTEITSN AT MILPVLA LA++ N HP+ LMVP Sbjct: 361 GKMGQMNGMSMILMILILVAMVNFLTEITSNLATTAMILPVLAPLAMSFNAHPFMLMVPV 420 Query: 475 AMAANCAFMLPVGTPPNAIIFASGKLKISEMVRTGFVINIFTLILIVGAVFYILPHLWGV 534 +AA+CAFMLPV TPPNA++F SG LKI +MV+ GF +NIF+++L+ +Y+L W Sbjct: 421 TVAASCAFMLPVATPPNAVVFGSGYLKIPDMVKAGFWMNIFSILLVTIVSYYLLDAFWNF 480 Query: 535 DLTVF 539 + VF Sbjct: 481 EADVF 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: 811 Number of extensions: 44 Number of successful extensions: 6 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: 491 Length adjustment: 35 Effective length of query: 511 Effective length of database: 456 Effective search space: 233016 Effective search space used: 233016 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 Apr 09 2024. 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