Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate Echvi_1519 Echvi_1519 Na+/H+-dicarboxylate symporters
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__Cola:Echvi_1519 Length = 444 Score = 340 bits (873), Expect = 4e-98 Identities = 194/436 (44%), Positives = 273/436 (62%), Gaps = 29/436 (6%) Query: 8 KIGLTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLV 67 KI L +I+IG+ G++ GL++ ++ DYI IGTIFIN LKM+ VPLV Sbjct: 4 KIPLHTQIIIGLVLGLVFGLIVIKTQMSPDFTMDYIKP-----IGTIFINGLKMIAVPLV 58 Query: 68 FISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNAS-------- 119 SL+ G +L + +KLGR+GGKT+ Y+ TT IA+ V + + PG + Sbjct: 59 LASLIVGVSNLGDITKLGRIGGKTIGAYMMTTVIAVTVGLLLVNVFAPGKSLPIETRERL 118 Query: 120 -------LASESMQYSAKEAPSLADVLINIVPSNPMKALSE-GNMLQIIIFAVIFGFAIS 171 + +S Q + + + L+++VP N A ++ G+MLQ++ FA+I G A+ Sbjct: 119 MEQFDDVVGDKSSQAAELKEQTPLKPLVDMVPENVFLAAADNGSMLQVVFFAIIVGIALL 178 Query: 172 HIGE-RGRRVAALFDDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLG-------METLE 223 I + + V A FD LN+VI+++V IM +APYGVFALM L + + +E L Sbjct: 179 EIPKSKASPVIAFFDGLNDVIIKIVGYIMLIAPYGVFALMASLIVEIAGDNPDSAIELLF 238 Query: 224 SVIKYFMLVLVVLLFHGFVVYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVT 283 +++KY +LV+ LL +VYPT+LKLF+ + F +R QL AFST+SS+ATLPVT Sbjct: 239 ALLKYSLLVVAGLLLMIVLVYPTILKLFTKVKYKDFFAALRPAQLLAFSTSSSSATLPVT 298 Query: 284 MEASEHRLGADNKVASFTLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMT 343 M+ E +G +V+SF LPLGATINMDGT + QGVA VFIAQ G+DL++T M+V+T Sbjct: 299 MKQVEEEIGVSEEVSSFVLPLGATINMDGTCLYQGVAAVFIAQALGLDLSLTQQLMIVLT 358 Query: 344 ATLASIGTAGVPGVGLVMLAMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATV 403 ATLASIGTAGVPG GL+ML +VL +G+P G+ALIL DR+LDM RT VNVTGD Sbjct: 359 ATLASIGTAGVPGAGLIMLLIVLESIGVPSAGLALILAPDRILDMFRTVVNVTGDATVCT 418 Query: 404 VIAKSEGALNEAVFND 419 V+A +EG L + + + Sbjct: 419 VVASTEGELPDGLIRE 434 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: 452 Number of extensions: 16 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: 437 Length of database: 444 Length adjustment: 32 Effective length of query: 405 Effective length of database: 412 Effective search space: 166860 Effective search space used: 166860 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: 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