Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate 7024548 Shewana3_1726 sodium:dicarboxylate symporter (RefSeq)
Query= TCDB::P96603 (421 letters) >FitnessBrowser__ANA3:7024548 Length = 437 Score = 238 bits (606), Expect = 3e-67 Identities = 130/403 (32%), Positives = 233/403 (57%), Gaps = 20/403 (4%) Query: 13 TAVIIGVIVGLVWP--DVGKE------MKPLGDTFINAVKMVIAPIIFFTIVLGIAKMGD 64 T + +G+I+ V+P D+ K+ + +G FI+++KM++ P++F ++V G + + Sbjct: 21 TGIALGLILRNVFPESDIVKDYITEGFLHVIGTIFISSLKMLVVPLVFISLVCGTCSLSE 80 Query: 65 MKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPG-AGLDYSKLEKGDVSQYTQNGGQG 123 K+G++GGK ++ T +ALI+ + ++ PG A L K+E YT Sbjct: 81 PSKLGRLGGKTLAFYLFTTAIALILAIVSAVLVHPGNASLASEKME------YTAKEAPS 134 Query: 124 IDWIEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKGKSVIDFFDKVSHVFF 183 + + + +IVP+N + A ++G++LQ++ F+++FG +A +GE+GK V F+ ++ V Sbjct: 135 LSSV--LINIVPTNPMQAMSEGNMLQIIIFAVIFGFAIAHIGERGKRVAALFEDLNEVIM 192 Query: 184 KIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFVFVALNIICKLY- 242 +++ IM+ AP G F MA GL + + + V + + + F+ + KL+ Sbjct: 193 RVVTLIMQLAPYGVFALMAKLALTLGLGTFESVVKYFFVVLVVLLIHAFIVYPTLLKLFS 252 Query: 243 GFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKME-RYGCSKSVVGLVIPTGYSFNLDG 301 G + ++R ++D L T+SS + LP ++ E R G + +P G + N+DG Sbjct: 253 GLNPLIFIRKMRDVQLFAFSTASSNATLPITIEASEHRLGVDNKIASFTLPLGATINMDG 312 Query: 302 TSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVLASTLSALQVI 361 T+I +ATVF+AQVFG++L+I +++ L S G AGV G G I+LA L+ + + Sbjct: 313 TAIMQGVATVFIAQVFGIELTITDYAAVVVTATLASIGTAGVPGVGLIMLAMVLNQVG-L 371 Query: 362 PLEGLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDE 404 P+EG+AL++GVDR + R VN+ G+ +AT+++AKSE EF+E Sbjct: 372 PVEGIALIIGVDRLLDMVRTAVNVTGDCVATVVIAKSEGEFNE 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: 452 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: 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