Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate Ac3H11_1083 C4-dicarboxylate transport protein
Query= SwissProt::P24943 (421 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1083 Length = 443 Score = 300 bits (767), Expect = 8e-86 Identities = 149/404 (36%), Positives = 253/404 (62%), Gaps = 6/404 (1%) Query: 9 QIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68 ++ + LI G+ +G ++ P A L+P+GD F++LIKM++ IV +V G+A GDLK Sbjct: 11 RVILALIAGVAIGLLW---PDTAVQLKPLGDGFIKLIKMLIPLIVFCVVVHGIAGTGDLK 67 Query: 69 KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNM--KSLEKTDIQSYVDTTNEVQ 126 ++G++G K++IYFE++TTIA+V+GL A F+PG G+N+ K+L+ + +Y D +++ Sbjct: 68 RVGRVGIKSLIYFEVVTTIALVLGLALAFWFEPGVGMNVDPKALDPKAMGAYADNASKLT 127 Query: 127 HHSMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAM 186 + + ++P + GD+L ++ FS++FG +A +G++G V + + + Sbjct: 128 GGGFSDFLLKLIPTTAVSAFANGDVLQVLLFSIVFGCALALMGDRGARVTGLIEDLSHVL 187 Query: 187 FYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVAKLF 246 F I+K AP GV I TV K+G+ SL L LV++ YA + F+ VVLG + ++ Sbjct: 188 FKTMGLIIKLAPLGVLGAIAFTVGKYGIGSLKQLGMLVVLFYAAVFIFVVVVLGLIMRVS 247 Query: 247 GINIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNLDGS 306 G ++F +++ L++EL + ++T SS++VLP+IM K+++ G + VIPTGYSFNLD Sbjct: 248 GFSLFKLLRYLREELAVVFATTSSDSVLPQIMAKLKHMGIRDSTVGLVIPTGYSFNLDAF 307 Query: 307 TLYQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTV-GIP 365 ++Y LAA+FIAQ + ++ +++L + +VTSKG GVPG + VVL ATL + IP Sbjct: 308 SIYITLAAVFIAQATNTPITMTDLLTILAISLVTSKGAHGVPGSAIVVLAATLHAIPAIP 367 Query: 366 IEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409 GL + +D + +AR N+IGN +A + ++ WEG + ++ Sbjct: 368 AIGLVLVLSVDWFMGIARALGNLIGNCVATVAIAAWEGDIDRDR 411 Lambda K H 0.326 0.143 0.404 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: 433 Number of extensions: 17 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: 443 Length adjustment: 32 Effective length of query: 389 Effective length of database: 411 Effective search space: 159879 Effective search space used: 159879 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