Align tonoplast dicarboxylate transporter (characterized)
to candidate GFF2170 HP15_2124 sodium: dicarboxylate cotransporter
Query= CharProtDB::CH_091173 (540 letters) >FitnessBrowser__Marino:GFF2170 Length = 493 Score = 270 bits (689), Expect = 1e-76 Identities = 155/466 (33%), Positives = 250/466 (53%), Gaps = 27/466 (5%) Query: 72 ARNMLGVLVWMFAWWLTEAVPMPITSMTPLFLFPLFGISAADDVANSYMDDVISLVLGSF 131 A + LG+++ M WW TEA+P+P T++ P+ L P G+ + Y + +I L LG F Sbjct: 50 AWSALGLMLLMATWWSTEAIPIPATALLPIVLVPALGLGTVGEATEPYANPIIFLFLGGF 109 Query: 132 ILALAVEHYNIHRRLALNITLVFCVEPLNAPLLLLGICATTAFVSMWMHNVAAAVMMMPV 191 L LA++ +N+HRR+AL +P + G TAF+SMW+ N A A+MM+P+ Sbjct: 110 TLGLAMQRWNLHRRIALMTLKAVGSKPRRQ---IAGFMLATAFLSMWVSNTATAIMMLPI 166 Query: 192 ATGILQRLPSSSSTTEVVHPAVGKFSRAVVLGVIYSAAVGGMSTLTGTGVNLILVGMWKS 251 ++ + ++ + V +++ A++L + YSA++GG++TL GT N +L + Sbjct: 167 GLSVVAMMDTNDNPE-----GVRRYATALLLAIAYSASIGGIATLIGTPPNALLA----A 217 Query: 252 YFPEADPIS--FSQWFFFGFPLALCIFVVLWCVLCVMYCPKGAGQALSPYLHKSHLRREL 309 Y E +S F+QW G P+ + + V+ W L + G S K+ +R+EL Sbjct: 218 YLSENQGVSVGFAQWMLLGVPVTIVMLVLAWWWLT----RRDFGLGNSGDGGKA-IRQEL 272 Query: 310 DLLGPMNFAEKMVLAVFGGLVVLWMTRNITDD-IPGWGRIFAGRAGDGTVSVMMATLLFI 368 + LG + EK+V VF W+ R + D + W D +++ A +F+ Sbjct: 273 EALGTLGKGEKLVALVFLVTASAWIFRPLLSDRLMPW-------LSDTGIAIAAAIAMFL 325 Query: 369 IPSNIKKGEKLMDWNKCKKLPWNIVLLLGAGFAIADGVRTSGLAEVLSKGLVFLETAPYW 428 IP N + E L+DW K +PW ++LL G G A+A + +SGLAE +++ L P Sbjct: 326 IPVNTRNREFLLDWETAKGIPWGVLLLFGGGLAMAGVISSSGLAEWIAQSLGVAGALPML 385 Query: 429 AIAPTVCLIAATITEFTSNNATTTLLVPLLIEIAKNMGIHPLLLMVPGAIGAQFAFLLPT 488 + V + +TE TSN AT +PLL +A + G+ PLLL VP AI A AF++P Sbjct: 386 VMILLVVGVIIFLTEVTSNTATAAAFLPLLGALALSQGVSPLLLTVPAAIAASCAFMMPV 445 Query: 489 GTPSNVVGFTTGHIEIKDMIKTGLPLKIAGTIFLSILMPTLGAYVF 534 TP N + F++GH++I DMI+ G L + G + +++L L VF Sbjct: 446 ATPPNAIVFSSGHMQIGDMIRAGFALNLLGIVVVTVLSYLLLGVVF 491 Lambda K H 0.326 0.140 0.441 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: 825 Number of extensions: 46 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: 540 Length of database: 493 Length adjustment: 35 Effective length of query: 505 Effective length of database: 458 Effective search space: 231290 Effective search space used: 231290 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 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 17 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