Align Na+/H+ dicarboxylate symporter (characterized, see rationale)
to candidate CCNA_01161 CCNA_01161 proton/sodium-glutamate symport protein
Query= uniprot:L0GT47 (419 letters) >FitnessBrowser__Caulo:CCNA_01161 Length = 448 Score = 231 bits (590), Expect = 3e-65 Identities = 148/406 (36%), Positives = 211/406 (51%), Gaps = 17/406 (4%) Query: 24 LIGLALGVAAGMAFGADAQLLAPIGTLFLNAIKMLIVPLVFVSLVAGITSMQDSAKLGRI 83 L+ LG A G A A+ L +G +F+ +++L+ PLVF ++VA I ++ R+ Sbjct: 31 LLARQLGPAEGQAGYVLAETLRQVGQIFVQLLRVLVPPLVFTAIVASIANIAQMQNAARL 90 Query: 84 SLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNMVASGNEQAKQAPSLVSILVGLVPANP 143 +T+ + VT +V IG+ G + PG ++ A+ + K S + L GLVP N Sbjct: 91 VWRTLFWFAVTALISVVIGIALGLVLQPGLHASLDAAAAKAPKTHGSWLDFLTGLVPVNI 150 Query: 144 VTAFAEG--------------NILQIIVFAIALGVSINLIGERGAPAVRLFDALAETFYK 189 + A N+LQI+V ++ GV+ +GE G ++ + K Sbjct: 151 LGLAASTKISDAGAASTSLSFNVLQIVVISLVTGVAALKVGEAGEAFLKFNASALAIVRK 210 Query: 190 LTDLVMRVAPIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGLLGLLAR 249 + V+R+ PIG L V +G L L IY A + VLLV +L L Sbjct: 211 VLWWVIRLTPIGTVGLFGNAVAQYGWTTLGQLGAFTVAIY-AGLGLVLLVVYPVLLALND 269 Query: 250 LNPLRFFQGIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDG- 308 LNP+RFFQG PA+ +AF + SS GTLPV+ LGV A F +P+GAT MDG Sbjct: 270 LNPIRFFQGAWPAIQLAFVSRSSIGTLPVTETVTETRLGVPRAYAAFAVPLGATTKMDGC 329 Query: 309 TAIYQGVLALFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAGLP 368 AIY + A+F+AQ FG+ L Y +I+ + + S TAG+ GA +ML L L+ GLP Sbjct: 330 AAIYPAIAAIFVAQFFGVHLVWSDYLLIVFVSVIGSAATAGLTGA-TVMLTLTLSTLGLP 388 Query: 369 LEGVALIAGIDRILDMARTTVNVAGDLMTTTLVGRSEQELDRAIYD 414 LEG L+ ID ILDM RT VNVAG + TLV + E LD Y+ Sbjct: 389 LEGAGLLLAIDPILDMGRTAVNVAGQALVPTLVAKREGILDLEAYN 434 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: 524 Number of extensions: 38 Number of successful extensions: 6 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: 448 Length adjustment: 32 Effective length of query: 387 Effective length of database: 416 Effective search space: 160992 Effective search space used: 160992 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 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