Align Na+/H+ dicarboxylate symporter (characterized, see rationale)
to candidate N515DRAFT_0019 N515DRAFT_0019 Na+/H+-dicarboxylate symporter
Query= uniprot:L0GT47 (419 letters) >FitnessBrowser__Dyella79:N515DRAFT_0019 Length = 438 Score = 250 bits (638), Expect = 7e-71 Identities = 163/442 (36%), Positives = 238/442 (53%), Gaps = 43/442 (9%) Query: 7 LSAPLRLLVRLPLWQQILIGLALGVAAGMAFGADAQ---------------LLAPIGTLF 51 +S P RL R IL GL +GV A +A A Q +L P+G +F Sbjct: 1 MSTPNRLATR------ILQGLLIGVVAAIATLAIGQFHPATLKTMQAFATAVLDPLGQVF 54 Query: 52 LNAIKMLIVPLVFVSLVAGITSMQDSAKLGRISLKTIAIYLVTTAFAVSIGLLFGALFSP 111 L + +++PLVF SL +G+ + +LG ++ +T A++ AV+IGLL L P Sbjct: 55 LRLLFFVVIPLVFASLASGVAQLGRLGRLGPLAARTFALFAANMLIAVAIGLLMMNLLQP 114 Query: 112 GEGMNMVASGN-------------EQAKQAP--SLVSILVGLVPANPVTAF------AEG 150 G + + E+ +Q P SL + + +P N + AF A G Sbjct: 115 GHQLEPGSRERLLQEYGGGAHRAMERRQQQPDMSLATAVDMFMPRNLLGAFVGHDRGALG 174 Query: 151 NILQIIVFAIALGVSINLIGERGAPAVRL-FDALAETFYKLTDLVMRVAPIGVFALTAGV 209 ++L +I+FAI +G + L+ E ++ D L+E + +R+AP+ V A+ V Sbjct: 175 DVLPLILFAILVGAAATLLDEDKRLKLQSGLDLLSELMTGIVGFALRLAPVAVPAMIYSV 234 Query: 210 VGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGLLGLLARLNPLRFFQGIAPALAVAFST 269 + G VLL L+ LA H+ L LLAR +PL +F+ I P L AFST Sbjct: 235 IVKIGTGVLLTLSVFTAGCALALALHLFGSLSLWLRLLARRSPLAYFRQIRPVLITAFST 294 Query: 270 SSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGTAIYQGVLALFIAQAFGIDLS 329 SSSS TLP S+ AR L + AGFVLP+GAT+NM GTA+++G + LF+AQAFG+DL+ Sbjct: 295 SSSSATLPASLALARDELRLRPSTAGFVLPLGATMNMSGTALFEGCVVLFVAQAFGVDLT 354 Query: 330 AGQYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAGLPLEGVALIAGIDRILDMARTTV 389 GQ +++L A L+++ AGIPG L ++ +L G+P EG+ L+ G+DRILDM RTTV Sbjct: 355 LGQQCVLMLLAVLSAVAVAGIPGGSLPLIAGLLATFGVPPEGIGLVLGVDRILDMLRTTV 414 Query: 390 NVAGDLMTTTLVGRSEQELDRA 411 NV DL+T T+V D A Sbjct: 415 NVGSDLVTATVVDAGAVRGDHA 436 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: 554 Number of extensions: 30 Number of successful extensions: 2 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: 438 Length adjustment: 32 Effective length of query: 387 Effective length of database: 406 Effective search space: 157122 Effective search space used: 157122 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 Apr 09 2024. 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