Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate WP_083492058.1 ABB28_RS15865 dicarboxylate/amino acid:cation symporter
Query= TCDB::P96603 (421 letters) >NCBI__GCF_001431535.1:WP_083492058.1 Length = 440 Score = 190 bits (483), Expect = 6e-53 Identities = 124/410 (30%), Positives = 215/410 (52%), Gaps = 28/410 (6%) Query: 17 IGVIVGLVWPDVGKEMKPLGDT---------------FINAVKMVIAPIIFFTIVLGIAK 61 IG+++GLV +G + L D F+N + M+I P+IF +V+G+++ Sbjct: 23 IGLVLGLVVHALGAQTPALMDAAKWLMHYITTPASGLFLNLIFMLIVPLIFSALVMGVSE 82 Query: 62 MGDMKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYS--------KLEKGDV 113 MGD++ +G++G K Y V++++A+ IGL +VN++KPG G+D + LE+ Sbjct: 83 MGDIRALGRIGWKTLAYTIVLSSIAVAIGLVLVNLLKPGVGVDPAMANQILAENLERS-- 140 Query: 114 SQYTQNGGQGIDWIEFITHIVPSNMVDAFAK-GDILQVLFFSILFGVGLAALG-EKGKSV 171 + G ++ + IVPSN+V+A + G IL ++FF+++FG+G+ EK + Sbjct: 141 KEIVAGVGSQPKGMDMLLSIVPSNIVEAASSNGAILSLMFFALMFGIGMVLTDDEKVAPL 200 Query: 172 IDFFDKVSHVFFKIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFV 231 + + V +I ++R AP M FG + + L + + V + + L + Sbjct: 201 RRAIEGIFEVSMTLINLVIRLAPYAVACFMFNLAALFGFELLIRLGAYVGVVVLALGLHM 260 Query: 232 FVALNIICKLYGFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKMERYGCSKSVVGLVI 291 V + L G S + R ++ ++ T+SS + LP + + G + V V+ Sbjct: 261 VVTYGVAVWLSGRSPLAFFRDTQEATVMAFSTASSNATLPTALRVADEMGLPQKVSRFVL 320 Query: 292 PTGYSFNLDGTSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVL 351 G + N +GT+++ + +FLAQ FGVDLSIGQQI ++ V +L G AGV V+ Sbjct: 321 TVGATANQNGTALFEGVTVIFLAQFFGVDLSIGQQIMVMAVCILGGIGTAGVPSGSLPVV 380 Query: 352 ASTLSALQVIPLEGLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENE 401 A + + V PL G+ L+LGV+ F+ R +N+ G+ T +VAK E + Sbjct: 381 AMICAMVGVNPL-GIGLILGVNHFLDMCRTALNVTGDLALTTLVAKGEKD 429 Lambda K H 0.326 0.143 0.408 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: 459 Number of extensions: 24 Number of successful extensions: 5 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: 421 Length of database: 440 Length adjustment: 32 Effective length of query: 389 Effective length of database: 408 Effective search space: 158712 Effective search space used: 158712 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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