Align Na+/H+ dicarboxylate symporter (characterized, see rationale)
to candidate Ga0059261_3350 Ga0059261_3350 Na+/H+-dicarboxylate symporters
Query= uniprot:L0GT47 (419 letters) >FitnessBrowser__Korea:Ga0059261_3350 Length = 436 Score = 308 bits (788), Expect = 3e-88 Identities = 171/404 (42%), Positives = 241/404 (59%), Gaps = 5/404 (1%) Query: 19 LWQQILIGLALGVAAGMAFGADAQLLAPIGTLFLNAIKMLIVPLVFVSLVAGITSMQDSA 78 LW++IL L LG AG+A+G A +A IG LF+ I+ML+VPLVF+++ AG+ ++ D Sbjct: 31 LWRRILGALVLGAIAGVAWGPGATSIAWIGELFVRLIRMLVVPLVFLTIAAGVAALADPK 90 Query: 79 KLGRISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNMVASGNEQAKQAPSLVSILVGL 138 +LG I +KT+A+Y+ TT AV+ GL+ L PG G + + P + + + Sbjct: 91 RLGSIGVKTLAMYVFTTTLAVTTGLIVATLIGPGIGASFADAVPRAMGTPPDTARMFMEI 150 Query: 139 VPANPVTAFAEGNILQIIVFAIALGVSINLIGERGAPAVRLFDALAETFYKLTDLVMRVA 198 +P NPV A A+G L +I FAI +G + G+ P + ++ K+ VM A Sbjct: 151 IPDNPVGAMADGKTLSVIFFAILVGAGVIAAGKGAEPVRAFLNGASDVMLKIVGFVMETA 210 Query: 199 PIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGL-LGLLARLNPLRFFQ 257 P GVFAL A V+G+ G L + + + S LL++G + + L+A L+PL FF+ Sbjct: 211 PFGVFALIAVVMGTSGPASFLAILKLAICVVAGSAVVTLLIHGLIVVRLMAWLSPLPFFR 270 Query: 258 GIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGTAIYQGVLA 317 GIA A+ V FSTSSSS TLPV+I A+ NLG+S+ VA VLP+GATI MDG A+Y +L Sbjct: 271 GIADAIMVGFSTSSSSATLPVAIRVAQNNLGISKPVASTVLPLGATIGMDGAAMYVAMLT 330 Query: 318 LFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAGLPLEGVALIAG 377 LF AQAFG+DL+ Y +I T T+ ++G A +P L +L VL A G+ E AL+ G Sbjct: 331 LFSAQAFGLDLTWADYLVIAATTTIVAMGVAPVPSGSLFVLAAVLHAIGITPEQTALVVG 390 Query: 378 ----IDRILDMARTTVNVAGDLMTTTLVGRSEQELDRAIYDSSN 417 DRILDM RT NV DL T V R E E+D +Y+S+N Sbjct: 391 FVLPFDRILDMTRTVPNVTSDLAIATAVARWEGEMDVTVYNSAN 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: 574 Number of extensions: 35 Number of successful extensions: 3 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: 436 Length adjustment: 32 Effective length of query: 387 Effective length of database: 404 Effective search space: 156348 Effective search space used: 156348 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