Align Na+/H+ dicarboxylate symporter (characterized, see rationale)
to candidate WP_083492058.1 ABB28_RS15865 dicarboxylate/amino acid:cation symporter
Query= uniprot:L0GT47 (419 letters) >NCBI__GCF_001431535.1:WP_083492058.1 Length = 440 Score = 253 bits (646), Expect = 8e-72 Identities = 157/422 (37%), Positives = 241/422 (57%), Gaps = 32/422 (7%) Query: 16 RLPLWQQILIGLALGVAAGM---AFGADAQLL------------APIGTLFLNAIKMLIV 60 ++PL ++ IG A+G+ G+ A GA L P LFLN I MLIV Sbjct: 10 KMPLHWKMGIGFAIGLVLGLVVHALGAQTPALMDAAKWLMHYITTPASGLFLNLIFMLIV 69 Query: 61 PLVFVSLVAGITSMQDSAKLGRISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMN---- 116 PL+F +LV G++ M D LGRI KT+A +V ++ AV+IGL+ L PG G++ Sbjct: 70 PLIFSALVMGVSEMGDIRALGRIGWKTLAYTIVLSSIAVAIGLVLVNLLKPGVGVDPAMA 129 Query: 117 --MVASGNEQAKQA-------PSLVSILVGLVPANPV-TAFAEGNILQIIVFAIALGVSI 166 ++A E++K+ P + +L+ +VP+N V A + G IL ++ FA+ G+ + Sbjct: 130 NQILAENLERSKEIVAGVGSQPKGMDMLLSIVPSNIVEAASSNGAILSLMFFALMFGIGM 189 Query: 167 NLIG-ERGAPAVRLFDALAETFYKLTDLVMRVAPIGVFALTAGVVGSHGAEVLLPLAGVI 225 L E+ AP R + + E L +LV+R+AP V + G E+L+ L + Sbjct: 190 VLTDDEKVAPLRRAIEGIFEVSMTLINLVIRLAPYAVACFMFNLAALFGFELLIRLGAYV 249 Query: 226 GVIYLASIAHVLLVYGGLLGLLARLNPLRFFQGIAPALAVAFSTSSSSGTLPVSIECARK 285 GV+ LA H+++ YG + L R +PL FF+ A +AFST+SS+ TLP ++ A + Sbjct: 250 GVVVLALGLHMVVTYGVAVWLSGR-SPLAFFRDTQEATVMAFSTASSNATLPTALRVADE 308 Query: 286 NLGVSEGVAGFVLPVGATINMDGTAIYQGVLALFIAQAFGIDLSAGQYAMIILTATLASI 345 +G+ + V+ FVL VGAT N +GTA+++GV +F+AQ FG+DLS GQ M++ L I Sbjct: 309 -MGLPQKVSRFVLTVGATANQNGTALFEGVTVIFLAQFFGVDLSIGQQIMVMAVCILGGI 367 Query: 346 GTAGIPGAGLIMLGLVLTAAGLPLEGVALIAGIDRILDMARTTVNVAGDLMTTTLVGRSE 405 GTAG+P L ++ ++ G+ G+ LI G++ LDM RT +NV GDL TTLV + E Sbjct: 368 GTAGVPSGSLPVVAMICAMVGVNPLGIGLILGVNHFLDMCRTALNVTGDLALTTLVAKGE 427 Query: 406 QE 407 ++ Sbjct: 428 KD 429 Lambda K H 0.324 0.140 0.386 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: 563 Number of extensions: 32 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: 419 Length of database: 440 Length adjustment: 32 Effective length of query: 387 Effective length of database: 408 Effective search space: 157896 Effective search space used: 157896 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: 41 (22.0 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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