Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate H281DRAFT_01363 H281DRAFT_01363 aerobic C4-dicarboxylate transport protein
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__Burk376:H281DRAFT_01363 Length = 433 Score = 332 bits (851), Expect = 1e-95 Identities = 153/405 (37%), Positives = 265/405 (65%), Gaps = 5/405 (1%) Query: 6 LAWQIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVG 65 L + +F +I+G+++G + P +A ++P+GD F++LIKM++ PI+ ++V G+A +G Sbjct: 22 LYFHVFAAIIIGVLLG---HFAPSLAVKMKPLGDAFIKLIKMVIGPIIFCTVVTGIAGMG 78 Query: 66 DLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMKSLEKTDIQSYVDTTNEV 125 D+KK+G++GGK ++YFEI++T+++V+GL+A +IF PG+G N+ D ++ T Sbjct: 79 DMKKVGRVGGKALLYFEIVSTLSLVIGLVAGHIFHPGSGFNLDPAT-IDTKALAGYTTAA 137 Query: 126 QHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEA 185 + VE ++I+P + + ++G++L I+ SV+FG +AA GE+G+P++ A Sbjct: 138 HQQNTVEFLMHIIPDTVTGAFASGNVLQILLISVLFGAALAATGERGRPLIAMIDYFAHT 197 Query: 186 MFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVAKL 245 F + + IMK A G F I T+ +G+ +++PL KL+ YAT+ F+ VLG +++L Sbjct: 198 FFGIVHIIMKVAAIGAFGSIAFTIGTYGIGAVVPLLKLIGAFYATLAVFVIVVLGAISRL 257 Query: 246 FGINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNLDG 305 G +IF + +++E+++ T+SSE LP++++K+E+ GC K++ VIP GYSFNLDG Sbjct: 258 LGFSIFRFMSYIREEILIVLGTSSSEAALPQMLEKLERLGCSKSVVGLVIPAGYSFNLDG 317 Query: 306 STLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG-I 364 + +Y +A +FIAQ + I++S++QQ++L+ V M+TSKG +GV G +FV+L +TL I Sbjct: 318 TNIYLTMAVLFIAQAFNIELSLTQQLTLVGVAMLTSKGASGVAGAAFVMLTSTLLVFPLI 377 Query: 365 PVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409 PV G+ I GI R + N IGN +A +++S WE + + K Sbjct: 378 PVSGMVLILGIHRFMGTGLAIANTIGNGVATLVVSAWEHELDRSK 422 Lambda K H 0.326 0.143 0.402 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: 430 Number of extensions: 18 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: 421 Length of database: 433 Length adjustment: 32 Effective length of query: 389 Effective length of database: 401 Effective search space: 155989 Effective search space used: 155989 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 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