Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate CA265_RS15560 CA265_RS15560 glutamate/aspartate:proton symporter GltP
Query= TCDB::P96603 (421 letters) >FitnessBrowser__Pedo557:CA265_RS15560 Length = 428 Score = 509 bits (1310), Expect = e-149 Identities = 251/411 (61%), Positives = 326/411 (79%), Gaps = 1/411 (0%) Query: 2 KLFKNLTVQVITAVIIGVIVGLVWPDVGKEMKPLGDTFINAVKMVIAPIIFFTIVLGIAK 61 K+F NLT QV+ A+IIG+ VG +P K + FIN + M+IAPIIFFTIVLGIA Sbjct: 9 KVFSNLTFQVLLAIIIGIYVGAYFPGFAPTAKLISQGFINLISMLIAPIIFFTIVLGIAH 68 Query: 62 MGDMKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYSKLEKGDVSQYTQNGG 121 MGDMKKVG+VGGKA +YFE+V+T+A+ IGL V N++KPGAG+ + ++ Y + Sbjct: 69 MGDMKKVGRVGGKALLYFEIVSTVAIAIGLLVANVLKPGAGMIAKAGDATKIAGYAEQA- 127 Query: 122 QGIDWIEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKGKSVIDFFDKVSHV 181 + ++W EF HI+P N++ +FA+G+ILQ+L F+ILFG GL LG +G +V++ FDK+S V Sbjct: 128 KDMNWAEFFLHIIPHNIIASFAEGNILQILLFAILFGYGLNKLGGEGTTVLNAFDKISKV 187 Query: 182 FFKIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFVFVALNIICKL 241 FKI+ IMR APIGAFG MA++IG GL+SI +A LM SVY+T FLF+FV LN IC+ Sbjct: 188 LFKIMKLIMRLAPIGAFGGMAFSIGTHGLESIVGMAKLMGSVYLTCFLFIFVILNGICRY 247 Query: 242 YGFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKMERYGCSKSVVGLVIPTGYSFNLDG 301 Y FSLW YL++I+ E+LIVLGTSSSES LP MM KME GC KSVVGLVIPTGYSFNLDG Sbjct: 248 YNFSLWAYLKYIRQEILIVLGTSSSESALPSMMQKMEAIGCDKSVVGLVIPTGYSFNLDG 307 Query: 302 TSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVLASTLSALQVI 361 T+IYL+MA +FL QVF VDL++GQQIT++ VLM+TSKGAAGVTGSGFIVL STL+AL+++ Sbjct: 308 TAIYLAMAVIFLCQVFHVDLTLGQQITVLGVLMITSKGAAGVTGSGFIVLVSTLTALKIM 367 Query: 362 PLEGLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDEAKSIEAVE 412 P+E +++L+GVDRFMSE RAI N+IGNG+ATI++AKSE +FDE K ++A++ Sbjct: 368 PIEHISILIGVDRFMSEARAITNVIGNGVATIVIAKSEKQFDEQKYLKAIQ 418 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: 563 Number of extensions: 21 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: 421 Length of database: 428 Length adjustment: 32 Effective length of query: 389 Effective length of database: 396 Effective search space: 154044 Effective search space used: 154044 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 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