Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate N515DRAFT_0013 N515DRAFT_0013 aerobic C4-dicarboxylate transport protein
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Dyella79:N515DRAFT_0013 Length = 433 Score = 493 bits (1269), Expect = e-144 Identities = 254/426 (59%), Positives = 330/426 (77%), Gaps = 3/426 (0%) Query: 8 YKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQ 67 ++ YF V+ AI G L+GH+ P+TGVALKPLGDGFI L+KM+I PIIF TVV GIAG+ Sbjct: 5 FRHFYFWVLAAIVAGGLIGHYAPETGVALKPLGDGFIALVKMLIGPIIFLTVVLGIAGVS 64 Query: 68 NMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAGK 127 ++K VG+ G A+LYFE+VS+ AL+IGLVVVN ++PG G + ++LDA+ VA Y A Sbjct: 65 DVKKVGRVGAKAILYFEVVSSFALVIGLVVVNTLKPGAGFNATPASLDATAVAKYANAAH 124 Query: 128 DQSIVGFILNVIPNTIVGAFA-NGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHV 186 +Q V F+L++IP T AF+ +GD+LQVL+ +++FGFA+ LG +PV+ F++ + V Sbjct: 125 EQGTVPFLLHLIPKTFSDAFSGDGDLLQVLLLALLFGFAMIHLGERARPVMTFLEALSKV 184 Query: 187 MFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICRA 246 F I+ MIM+LAP+GA+GAMAFTIG YGV SL L +LM FY+ C+LFV+VVLGAI RA Sbjct: 185 FFRIMGMIMRLAPLGAMGAMAFTIGKYGVHSLGPLLKLMGSFYLACILFVVVVLGAIARA 244 Query: 247 HGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDG 306 GFS+ K +RYIREELL+VLGTSSSESAL ++ K+ERLG KSVVGLV+P+GYSFNLDG Sbjct: 245 TGFSIFKFLRYIREELLLVLGTSSSESALVPLMQKLERLGCSKSVVGLVVPSGYSFNLDG 304 Query: 307 TSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 366 T+IYLTMAA+F+AQA + ++ ++TLL V +L+SKGA+GVTG+GFI LAATL+ V + Sbjct: 305 TNIYLTMAAIFVAQALGVELTLSQELTLLAVAMLTSKGASGVTGAGFITLAATLAVVPSV 364 Query: 367 PVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGGRAISDT 426 PVAGL+LILGIDRFMSEARA+TN++GN VATVVV+ W KELD LQA L GR+ S Sbjct: 365 PVAGLSLILGIDRFMSEARAITNIIGNGVATVVVSHWEKELDHASLQAAL--DGRSPSPA 422 Query: 427 REEDDL 432 +E L Sbjct: 423 ADEAPL 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: 603 Number of extensions: 23 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: 433 Length adjustment: 32 Effective length of query: 412 Effective length of database: 401 Effective search space: 165212 Effective search space used: 165212 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