Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate N515DRAFT_0019 N515DRAFT_0019 Na+/H+-dicarboxylate symporter
Query= TCDB::Q01857 (444 letters) >FitnessBrowser__Dyella79:N515DRAFT_0019 Length = 438 Score = 162 bits (409), Expect = 3e-44 Identities = 120/412 (29%), Positives = 206/412 (50%), Gaps = 31/412 (7%) Query: 27 LVAIAAGILLGHFYPE-LGTQ-------LKPLGDAFIKLVKMIIAPVIFLTVATGIAGMS 78 +VA A + +G F+P L T L PLG F++L+ ++ P++F ++A+G+A + Sbjct: 19 VVAAIATLAIGQFHPATLKTMQAFATAVLDPLGQVFLRLLFFVVIPLVFASLASGVAQLG 78 Query: 79 DLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVATFAAKAH 138 L ++G +A + F +A+ IGL++ N++QPG ++P S + + + AH Sbjct: 79 RLGRLGPLAARTFALFAANMLIAVAIGLLMMNLLQPGH--QLEPGSRE-RLLQEYGGGAH 135 Query: 139 ----------EQSIVGFLTNIIPTTIVGAF------ADGDILQVLFFSVLFGIALAMVGE 182 + S+ + +P ++GAF A GD+L ++ F++L G A ++ E Sbjct: 136 RAMERRQQQPDMSLATAVDMFMPRNLLGAFVGHDRGALGDVLPLILFAILVGAAATLLDE 195 Query: 183 -KGEQVVNFLNSLTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYI 241 K ++ + L+ L+ + +V ++ AP+ + I K G G + L++ + Sbjct: 196 DKRLKLQSGLDLLSELMTGIVGFALRLAPVAVPAMIYSVIVKIGTGVLLTLSVFTAGCAL 255 Query: 242 TSLLFVFIVLGAVARYNGF-SIVALLRYIKEELLLVLGTSSSEAALPG-LMNKMEKAGCK 299 L +F L R S +A R I+ L+ TSSS A LP L ++ + Sbjct: 256 ALALHLFGSLSLWLRLLARRSPLAYFRQIRPVLITAFSTSSSSATLPASLALARDELRLR 315 Query: 300 RSVVGLVIPTGYSFNLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGI 359 S G V+P G + N+ GT ++ LF+AQA G+ L+ G Q +L+L+A+LS+ AGI Sbjct: 316 PSTAGFVLPLGATMNMSGTALFEGCVVLFVAQAFGVDLTLGQQCVLMLLAVLSAVAVAGI 375 Query: 360 TGAGFITLAATLSVVPSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVV 411 G G + L A L VP G+ L+LG+DR + R N+ + V VV Sbjct: 376 PG-GSLPLIAGLLATFGVPPEGIGLVLGVDRILDMLRTTVNVGSDLVTATVV 426 Lambda K H 0.324 0.139 0.393 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: 472 Number of extensions: 26 Number of successful extensions: 5 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: 444 Length of database: 438 Length adjustment: 32 Effective length of query: 412 Effective length of database: 406 Effective search space: 167272 Effective search space used: 167272 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: 40 (21.6 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