Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate Dsui_3158 Dsui_3158 Na+/H+ dicarboxylate symporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__PS:Dsui_3158 Length = 448 Score = 525 bits (1352), Expect = e-153 Identities = 268/429 (62%), Positives = 332/429 (77%), Gaps = 3/429 (0%) Query: 3 TRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSG 62 + +P YK LY QV+ AIA+G+ LG F+P+TG +KPLGD FIKLIKM+IAPIIF TVV G Sbjct: 2 SHKPFYKRLYVQVLFAIALGVALGAFFPETGATMKPLGDAFIKLIKMMIAPIIFATVVVG 61 Query: 63 IAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAY 122 IA M +MK VG+ G AL+YFE+VST+AL IGL+VVN++QPG GM++D STLD +A Y Sbjct: 62 IAKMGDMKEVGRVGLKALIYFEVVSTVALAIGLIVVNILQPGAGMNVDPSTLDTKAIANY 121 Query: 123 VTAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDR 182 A +QS F++N+IPN++V AFA G+ILQVL+FSV+FG AL RLG KP++ +D Sbjct: 122 AAAAHNQSTTDFLMNIIPNSVVDAFAKGEILQVLLFSVLFGLALSRLGDKAKPLVKILDE 181 Query: 183 FAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGA 242 F+H +F +I MIM APIGA GAMAFTIG YG+GSL QLG LM YITC LFV VVLG Sbjct: 182 FSHGLFGVIGMIMHFAPIGAFGAMAFTIGKYGIGSLKQLGFLMANVYITCALFVFVVLGL 241 Query: 243 ICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSF 302 I + GFS+LK + YI+EELLIVLGTSSSESALPRM+ K+E LG K VVG+VIPTGYSF Sbjct: 242 IAKFTGFSLLKFLAYIKEELLIVLGTSSSESALPRMMTKLENLGCHKPVVGMVIPTGYSF 301 Query: 303 NLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSA 362 NLDGTSIYLTMAA+FIAQA + + +T Q+T+L VLLL+SKGAA VTG GFI LAATL+ Sbjct: 302 NLDGTSIYLTMAAIFIAQALNVPLTLTEQLTILGVLLLTSKGAAAVTGGGFITLAATLAT 361 Query: 363 V-GHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGGR 421 + G LPV GLAL+LG+DRFMSEARA+TNL+GN VAT+VV+KW L+ D++ L G Sbjct: 362 LGGKLPVEGLALLLGVDRFMSEARAITNLIGNGVATIVVSKWENALNTDRMTRVL--NGE 419 Query: 422 AISDTREED 430 + + E + Sbjct: 420 TVEEADEPE 428 Lambda K H 0.326 0.142 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: 614 Number of extensions: 25 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: 444 Length of database: 448 Length adjustment: 32 Effective length of query: 412 Effective length of database: 416 Effective search space: 171392 Effective search space used: 171392 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