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_3555 Echvi_3555 anion transporter
Query= TCDB::Q65NC0 (546 letters) >FitnessBrowser__Cola:Echvi_3555 Length = 485 Score = 509 bits (1312), Expect = e-149 Identities = 252/485 (51%), Positives = 338/485 (69%), Gaps = 8/485 (1%) Query: 57 QKIGLLLGPALFFAVLLFFFPEGLSYEGRMVLATTLWVAVWWITEAVPIPAASLLPIVLL 116 ++ GL+LGP F ++LFF P+GL+YE + VLA +W+A+WWI EA+PI A +LLP+V+L Sbjct: 7 KRSGLVLGPVAFLLIVLFFNPDGLTYEAQAVLALAVWMAIWWILEAIPIAATALLPLVIL 66 Query: 117 PLTGALEGAAVTSSYGDPIVFLFLGGFLIALAMERWNLHKRIALNIISVVGTSTSRIVLG 176 PLTGAL + Y DP V L++GGF+IA+ +E+WNLHKRIAL+IIS++GT IVLG Sbjct: 67 PLTGALSMDESAAPYADPKVLLYMGGFMIAVTIEKWNLHKRIALSIISLIGTDMRFIVLG 126 Query: 177 FMAATGFLSMWVSNTAAVMMMLPIGTAIIHQVSAVIKSERKDLAAEEAKFSKALIFSIGY 236 FM AT LSMW+SNTA +MMLPI A+IHQ++ +++A + +AL+ I Y Sbjct: 127 FMLATALLSMWISNTATSLMMLPIAVAVIHQLA----DGSDEISA--TRIGQALMLGIAY 180 Query: 237 AGTIGGLGTLIGTPPNIILAANIKKLYGVEVSFGGWMAFAVPVVVILLVAVWLYLTKVAH 296 + +IGGL T+IGTP NI+L +K+LYG+E+ F WM +P+ + LL W YL VA+ Sbjct: 181 SASIGGLATIIGTPTNIVLVGIVKELYGIEIGFAEWMLVGLPISLGLLGICWWYLVSVAY 240 Query: 297 PI-KMKELPGGKELILEEKRKLGKMSFEETMVLLVFGFAAFMWVTRTFLWDDKIPGIDDT 355 P K L GGK I + +G +S E VLLVF +F W+TR FL D +P ++DT Sbjct: 241 PFPKNMSLAGGKVEIQRQLAAIGPISKPEIRVLLVFLLVSFSWITRVFL-QDLLPFLNDT 299 Query: 356 MIAIFAASLLFLIPSLNKGGRVLDWSVSKDLPWGILLLFGGGLALATGFKETGLAEWIGG 415 +IA+ LLF++PS R+LDW ++D+PWGILLLFGGGLALA GFKETGLA W+G Sbjct: 300 IIALVGVLLLFMLPSSRGKKRLLDWKTAEDIPWGILLLFGGGLALAAGFKETGLAAWLGS 359 Query: 416 RLTVLDGFNFVVIVIISTALVLFLTEITSNTATATMILPVLASLALALNVHPYALMVPAA 475 L G +F++ ++I A V FLTEITSN ATA+M+LP+L ++ALAL VHPY LMV A Sbjct: 360 HFEALQGVHFLLFILIIVASVNFLTEITSNVATASMLLPILGAVALALGVHPYGLMVAAT 419 Query: 476 MAANCAFMLPVGTPPNAIIFASGKLKISEMVRTGFVINIFTLILIVGAVFYILPHLWGVD 535 MAA+CAFMLPV TPPNA++F SG L I M + G +NI ++ I V+YI+P LWG+D Sbjct: 420 MAASCAFMLPVATPPNAVVFGSGYLTIPAMAKAGLWMNILSIFFITLFVYYIMPFLWGID 479 Query: 536 LTVFP 540 L V+P Sbjct: 480 LKVYP 484 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: 42 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: 485 Length adjustment: 35 Effective length of query: 511 Effective length of database: 450 Effective search space: 229950 Effective search space used: 229950 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