Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate GFF1351 Psest_1386 Na+/H+-dicarboxylate symporters
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__psRCH2:GFF1351 Length = 409 Score = 275 bits (704), Expect = 1e-78 Identities = 154/403 (38%), Positives = 242/403 (60%), Gaps = 14/403 (3%) Query: 14 KILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFH---VIGTIFINSLKMLVVPLVFIS 70 +ILI G+ IG L G+ + EG + + G+IFI LKM+++PL+F S Sbjct: 7 QILIAACLGVAIGWLT-----GTLPTDAPVREGVLYASTLAGSIFIGLLKMVLIPLIFTS 61 Query: 71 LVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPG---NASLASESMQY 127 +V G +L ++ R+ G L ++ TT+ A++VA+ AA L +PG + L +E+M Sbjct: 62 IVVGVANLQAHHQVHRVWGGALVYFTLTTSAAMLVALVAANLFKPGAGLSLDLFAEAMND 121 Query: 128 SAKEAPSLADVLINIVPS---NPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRVAALF 184 +L + ++ + NP AL+ G++L +++FA+ G A+ G+R R + + Sbjct: 122 FEARQLTLPEFFLHFFANLFQNPFAALANGSILAVVVFAMFIGIALVAGGDRYRNILVVL 181 Query: 185 DDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHGFVVY 244 + E++MR+++ IM+LAP G+ AL+ KL + L +V + LV LFHG VV Sbjct: 182 QEFLELMMRIISWIMRLAPLGILALLIKLVAEQDVALLSAVGGFIALVFATTLFHGTVVL 241 Query: 245 PTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASFTLPL 304 P +L L +G SPL F R R+ + AF+T+SS ATLP+++ +E L +A F LPL Sbjct: 242 PGILFLATGKSPLWFFRGTREALITAFATSSSAATLPISLRCAEDNLKVRPGIAGFVLPL 301 Query: 305 GATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLVMLAM 364 GAT+NMDGTA+ + A +F+A + GI+L++ A+V TA +AS G G+P G+V + M Sbjct: 302 GATMNMDGTALYEAAAALFVANLMGIELSLAQQAVVFFTAMIASTGAPGIPSAGMVTMVM 361 Query: 365 VLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAK 407 VL VGLP E +A++L +DR+LD VRTAVNV GD + +VV+ + Sbjct: 362 VLQAVGLPAEAVAILLPIDRLLDTVRTAVNVEGDIIGSVVVQR 404 Lambda K H 0.325 0.139 0.388 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: 356 Number of extensions: 19 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: 437 Length of database: 409 Length adjustment: 32 Effective length of query: 405 Effective length of database: 377 Effective search space: 152685 Effective search space used: 152685 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 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 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