Align Na+/H+ dicarboxylate symporter (characterized, see rationale)
to candidate N515DRAFT_1080 N515DRAFT_1080 Na+/H+-dicarboxylate symporter
Query= uniprot:L0GT47 (419 letters) >FitnessBrowser__Dyella79:N515DRAFT_1080 Length = 422 Score = 308 bits (788), Expect = 3e-88 Identities = 161/397 (40%), Positives = 244/397 (61%), Gaps = 4/397 (1%) Query: 20 WQQILIGLALGVAAGMAFG-ADAQLLAPIGTLFLNAIKMLIVPLVFVSLVAGITSMQDSA 78 W+++L G LG AG G P+G +++ IKM+ VPLVF ++V ++S+ Sbjct: 13 WKRVLAGFVLGALAGWLCGPGSVAWFQPLGDVYVALIKMIAVPLVFFAVVNSVSSLHGVQ 72 Query: 79 KLGRISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNMVA-SGNEQAKQAPSLVSILVG 137 ++ + +T + +T A AV +GLL G L PG G+ + +G+ + ++ PS V +L+ Sbjct: 73 RMAALGGRTFLWFALTAALAVGVGLLVGHLTDPGLGVGQLTMAGDYKVREVPSAVKVLLD 132 Query: 138 LVPANPVTAFAEGNILQIIVFAIALGVSINLIGERGAPAVRLFDALAETFYKLTDLVMRV 197 +VP NP A +EG ILQ+I FA LG+++ IGE+ A LF + ++T V+ + Sbjct: 133 VVPTNPFRALSEGKILQVIFFAGLLGLALVKIGEKSARLRELFGEANDAMIQVTRFVLEM 192 Query: 198 APIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGLLGLLARLNPLRFFQ 257 PIG F L A +V +G E LLPL + +Y A +++VYGGLL L L+P RFF+ Sbjct: 193 TPIGTFGLIAALVAGYGFEKLLPLGKFVLALYAACAVQIVVVYGGLL-LAHGLSPRRFFR 251 Query: 258 GIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGT-AIYQGVL 316 G+ PA+ VAF++SSS ++PV++ +NLGVS A F +P+GA+I MDG AIY + Sbjct: 252 GVLPAMQVAFTSSSSFASMPVALRSVTQNLGVSPAYASFAVPLGASIKMDGCGAIYPAIS 311 Query: 317 ALFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAGLPLEGVALIA 376 ++F+AQ FG+ L QY +I+L + L S GTAG+PG +M+ LVL++AGLP+EG+ + Sbjct: 312 SIFVAQYFGLQLEPAQYFVILLASVLGSFGTAGVPGTATVMVTLVLSSAGLPVEGIGYLV 371 Query: 377 GIDRILDMARTTVNVAGDLMTTTLVGRSEQELDRAIY 413 IDR+LDM RT NV G ++ LV R + LD +Y Sbjct: 372 AIDRVLDMMRTMTNVTGQMLVPVLVAREQGLLDMDVY 408 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: 550 Number of extensions: 36 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: 422 Length adjustment: 32 Effective length of query: 387 Effective length of database: 390 Effective search space: 150930 Effective search space used: 150930 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: 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