Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate GFF4002 Psest_4075 Na+/H+-dicarboxylate symporters
Query= TCDB::P96603 (421 letters) >FitnessBrowser__psRCH2:GFF4002 Length = 419 Score = 253 bits (645), Expect = 1e-71 Identities = 140/400 (35%), Positives = 221/400 (55%), Gaps = 14/400 (3%) Query: 10 QVITAVIIGVIVGLVWPDVGKEMKPLGDTFINAVKMVIAPIIFFTIVLGIAKMGDMKKVG 69 Q++ + +GV G+ + + + P+G F+NA+KM+I P++F ++V GI M D K+G Sbjct: 22 QILIGLALGVAAGMAFGADAQLLAPIGTLFLNAIKMLIVPLVFVSLVAGITSMQDSAKLG 81 Query: 70 KVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYSKLEKGDVSQYTQNGGQGIDWIEF 129 ++ K + V T A+ IGL + PG G++ V+ + Q + Sbjct: 82 RISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNM-------VASGNEQAKQAPSLVSI 134 Query: 130 ITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKGKSVIDFFDKVSHVFFKIIGYI 189 + +VP+N V AFA+G+ILQ++ F+I GV + +GE+G + FD ++ F+K+ + Sbjct: 135 LVGLVPANPVTAFAEGNILQIIVFAIALGVSINLIGERGAPAVRLFDALAETFYKLTDLV 194 Query: 190 MRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFVFVALNIICKLYGFSLWNY 249 MR APIG F A +G G + + PLA ++ +Y+ V + + L + N Sbjct: 195 MRVAPIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGLLGL--LARLNP 252 Query: 250 LRF---IKDELLIVLGTSSSESVLPRMMD-KMERYGCSKSVVGLVIPTGYSFNLDGTSIY 305 LRF I L + TSSS LP ++ + G S+ V G V+P G + N+DGT+IY Sbjct: 253 LRFFQGIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGTAIY 312 Query: 306 LSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVLASTLSALQVIPLEG 365 + +F+AQ FG+DLS GQ IIL L S G AG+ G+G I+L L+A +PLEG Sbjct: 313 QGVLALFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAG-LPLEG 371 Query: 366 LALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDEA 405 +AL+ G+DR + R VN+ G+ + T +V +SE E D A Sbjct: 372 VALIAGIDRILDMARTTVNVAGDLMTTTLVGRSEQELDRA 411 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: 450 Number of extensions: 19 Number of successful extensions: 4 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: 419 Length adjustment: 32 Effective length of query: 389 Effective length of database: 387 Effective search space: 150543 Effective search space used: 150543 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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