Align Fumarate:H+ symporter of 442 aas and 14 established TMSs, DctA. Responsible for the transport of dicarboxylates such as succinate, fumarate, and malate (characterized)
to candidate BPHYT_RS16825 BPHYT_RS16825 C4-dicarboxylate ABC transporter
Query= TCDB::Q1J1H5 (442 letters) >FitnessBrowser__BFirm:BPHYT_RS16825 Length = 441 Score = 442 bits (1136), Expect = e-128 Identities = 227/415 (54%), Positives = 309/415 (74%), Gaps = 1/415 (0%) Query: 1 MPKIFRSLYVQVLIAIVLGILVGFLFPSFGEGLKPLGDGFIKLIKMLIAPIIFATVVSGI 60 M K F SL+ +V+IA+V GI+VG +FP F + L+PLGDGF+KLIKM+I PI+F VVSG+ Sbjct: 1 MLKFFNSLFGRVVIALVAGIVVGAVFPHFAQSLRPLGDGFLKLIKMVIGPIVFCVVVSGM 60 Query: 61 AHMRDTKKVGRVGGKALIYFEVVTTFALVIGLVVANILKPGHGMNVNPATLDTSAISKYT 120 AH D +KVGRVG KA+IYFEV+TT ALVIG ++A + +PG GMN++ +LD +++S YT Sbjct: 61 AHAGDLRKVGRVGLKAVIYFEVMTTIALVIGAILAYVTRPGVGMNIDLHSLDPASLSTYT 120 Query: 121 QAAGE-QSVADFLLHIIPNTLVSAFTEGDLLQVLLISVLFGFALTQLGTLGQKVLAGIEA 179 + A + A FLL IIP+T ++AF GD+LQ+L+ SVLFG AL+ LG Q+V + I+ Sbjct: 121 EHAKSLKDTAGFLLKIIPDTAINAFATGDILQILVFSVLFGSALSLLGNKAQRVSSLIDE 180 Query: 180 VNSAVFVILGFVMRLAPIGAFGAMAFTIGKYGVGTLAQLAYLMVAFYATCLLFVFVVLGL 239 ++ F ++GF+++LAP+G GA+AFT G YGV +L QL L++ FY +C +FV VVLG+ Sbjct: 181 LSQVFFRVMGFIIKLAPLGVLGAIAFTTGTYGVESLKQLGMLVLVFYLSCFVFVVVVLGV 240 Query: 240 IARFAGFSILKFIRFIKEELLLVLGTSSSESALPRLITKLEYAGANRSVVGLVVPAGYSF 299 + R AGFSI K IR+++EEL +VLGT+SS++ LP+++ KLE+ G S VGLV+P GYSF Sbjct: 241 VMRLAGFSIFKLIRYLREELSIVLGTASSDAVLPQIMRKLEWMGVKDSTVGLVIPTGYSF 300 Query: 300 NLDGTSIYLTMATLFIAQATNTHLSLGQQLGILGVLLLTSKGAAGVTGSGFITLAATLSA 359 NLDG SIYLT+A +FIAQATNT LS+ + ++ V L+TSKGA G+ GS + LAATLSA Sbjct: 301 NLDGFSIYLTLAVIFIAQATNTPLSVHDLIVVVLVSLVTSKGAHGIPGSAIVILAATLSA 360 Query: 360 VGHVPVAGLALILGIDRFMSEARALTNFVGNGVATLVIARSEKALDTNRLQRVLN 414 + +PV GL LIL +D F+ ARALTN +GN VAT+V+A E +D R RVLN Sbjct: 361 IPAIPVLGLVLILPVDWFVGIARALTNLIGNCVATVVVAVWENDIDRARAHRVLN 415 Lambda K H 0.325 0.142 0.398 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: 567 Number of extensions: 28 Number of successful extensions: 3 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: 442 Length of database: 441 Length adjustment: 32 Effective length of query: 410 Effective length of database: 409 Effective search space: 167690 Effective search space used: 167690 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: 51 (24.3 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