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 RR42_RS33745 RR42_RS33745 C4-dicarboxylate transporter
Query= TCDB::Q1J1H5 (442 letters) >FitnessBrowser__Cup4G11:RR42_RS33745 Length = 452 Score = 493 bits (1269), Expect = e-144 Identities = 241/417 (57%), Positives = 321/417 (76%) Query: 3 KIFRSLYVQVLIAIVLGILVGFLFPSFGEGLKPLGDGFIKLIKMLIAPIIFATVVSGIAH 62 ++ SLYVQVLIA+ GIL+G P G LKPLGD FI+LIKM+ APIIFATVV GIA Sbjct: 4 RLISSLYVQVLIAVAAGILLGIFMPHIGSALKPLGDIFIRLIKMVFAPIIFATVVLGIAK 63 Query: 63 MRDTKKVGRVGGKALIYFEVVTTFALVIGLVVANILKPGHGMNVNPATLDTSAISKYTQA 122 M K +GRVG +AL+YFEV++TFAL++G++V N+++PGHGMNV+PATLDT +I+ YT Sbjct: 64 MESMKDLGRVGWRALLYFEVLSTFALLLGVIVVNVVQPGHGMNVDPATLDTKSIAAYTAQ 123 Query: 123 AGEQSVADFLLHIIPNTLVSAFTEGDLLQVLLISVLFGFALTQLGTLGQKVLAGIEAVNS 182 + + DFLL+++P +++ A + D+LQ+L+ SV G AL LG G+ +A +++ + Sbjct: 124 VKHEGIMDFLLNLVPMSIMDALAKNDILQILVFSVFMGVALAHLGERGKPFVAALDSFAN 183 Query: 183 AVFVILGFVMRLAPIGAFGAMAFTIGKYGVGTLAQLAYLMVAFYATCLLFVFVVLGLIAR 242 A+F I+G +MR+AP+ AFGAM+FT+GKYG G++A L L+ Y TC LFV +VLG I R Sbjct: 184 AMFAIVGMIMRVAPVAAFGAMSFTVGKYGFGSIASLGKLVATMYGTCALFVLIVLGAICR 243 Query: 243 FAGFSILKFIRFIKEELLLVLGTSSSESALPRLITKLEYAGANRSVVGLVVPAGYSFNLD 302 GF + F+++IK+E+L VLGTSSSES +P+L+ KLE G ++ VVGLVVPAG +FN D Sbjct: 244 ICGFGLFNFLKYIKDEILTVLGTSSSESVIPQLMRKLENVGVSKPVVGLVVPAGLTFNPD 303 Query: 303 GTSIYLTMATLFIAQATNTHLSLGQQLGILGVLLLTSKGAAGVTGSGFITLAATLSAVGH 362 G IY TMA +FIAQATNT L+L Q +LGVLLLTSKG+AG+TGSGFITLAATL+++G Sbjct: 304 GQCIYYTMAAIFIAQATNTPLTLTDQFVVLGVLLLTSKGSAGITGSGFITLAATLASLGK 363 Query: 363 VPVAGLALILGIDRFMSEARALTNFVGNGVATLVIARSEKALDTNRLQRVLNGEVLP 419 +PVAG+ L+LG+DRFMSEARA+TN +GN VAT+ IA+ ALD +R+QRVLNGEV P Sbjct: 364 IPVAGMVLLLGVDRFMSEARAITNTIGNAVATMAIAKWVGALDEDRVQRVLNGEVDP 420 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: 586 Number of extensions: 25 Number of successful extensions: 2 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: 452 Length adjustment: 33 Effective length of query: 409 Effective length of database: 419 Effective search space: 171371 Effective search space used: 171371 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