Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate 201109 SO1948 sodium:dicarboxylate symporter family protein (NCBI ptt file)
Query= TCDB::P96603 (421 letters) >FitnessBrowser__MR1:201109 Length = 437 Score = 238 bits (608), Expect = 2e-67 Identities = 133/413 (32%), Positives = 233/413 (56%), Gaps = 20/413 (4%) Query: 3 LFKNLTVQVITAVIIGVIVGLVWPD--------VGKEMKPLGDTFINAVKMVIAPIIFFT 54 L + + + T +I G+I+ ++PD + +G FI+++KM++ P++F + Sbjct: 11 LTSKILIGMATGIIFGLILRNLFPDSIFIKDYITDGFLHVIGTIFISSLKMLVVPLVFIS 70 Query: 55 IVLGIAKMGDMKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPG-AGLDYSKLEKGDV 113 +V G + + K+G++GGK ++ T LAL++ +F I+ PG A L KL Sbjct: 71 LVCGTCSLSEPSKLGRLGGKTLAFYLFTTVLALVLAVFAAVIVHPGDATLANEKLN---- 126 Query: 114 SQYTQNGGQGIDWIEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKGKSVID 173 Y + + + I ++P+N V A ++G++LQ++ F+++FG +A LGE+G + Sbjct: 127 --YVAK--EAPSFAQVIIDMMPTNPVQAMSEGNMLQIIIFAVIFGFAIAHLGERGNRIAQ 182 Query: 174 FFDKVSHVFFKIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFVFV 233 FD +++V +++ +M+ AP G F MA GL++ + V + + FV Sbjct: 183 LFDDLNNVIMRVVTLVMQLAPYGVFALMAKLALTLGLETFGSVVKYFFLVLTLLLIHNFV 242 Query: 234 ALNIICKLY-GFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKME-RYGCSKSVVGLVI 291 +I+ K + G + ++R ++D L T+SS + LP ++ E R G + + Sbjct: 243 TYSILLKAFSGLNPLIFIRKMRDVQLFAFSTASSNATLPITIEASEHRLGVDNKIASFTL 302 Query: 292 PTGYSFNLDGTSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVL 351 P G + N+DGT+I +ATVF+AQVFG++LS+ +I+ L S G AGV G G I+L Sbjct: 303 PLGATINMDGTAIMQGVATVFIAQVFGIELSLTDYAAVIVTATLASIGTAGVPGVGLIML 362 Query: 352 ASTLSALQVIPLEGLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDE 404 A L+ + +P+EG+AL++GVDR + R VN+ G+ +AT+I+AKSE EF+E Sbjct: 363 AMVLNQVG-LPVEGIALIIGVDRLLDMVRTAVNVTGDCVATVIIAKSEGEFNE 414 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: 437 Number of extensions: 20 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: 437 Length adjustment: 32 Effective length of query: 389 Effective length of database: 405 Effective search space: 157545 Effective search space used: 157545 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