Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate WP_035131390.1 Q763_RS03785 cation:dicarboxylase symporter family transporter
Query= TCDB::Q848I3 (444 letters) >NCBI__GCF_000769915.1:WP_035131390.1 Length = 470 Score = 296 bits (757), Expect = 1e-84 Identities = 158/401 (39%), Positives = 246/401 (61%), Gaps = 8/401 (1%) Query: 9 KSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQN 68 +SL ++V + IG +GH +P+ G L+ L F+KLIK ++ P+IF T+V GIAG N Sbjct: 55 RSLTTWILVCLVIGAAIGHEWPEAGQGLQVLSKIFLKLIKTIVGPLIFATLVYGIAGHSN 114 Query: 69 MKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAGKD 128 +K VG+ G +LLYFEIV+T+AL IGL +N+ + G G+ + + + + A + Sbjct: 115 IKQVGRMGWKSLLYFEIVTTLALFIGLAAINITKAGEGI------IQPTDIKETIQAAEP 168 Query: 129 QSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVL-DFIDRFAHVM 187 Q+ IL++ P I + A G++LQ+++FSVIFG AL + + V+ DF + VM Sbjct: 169 QTWQQIILHIFPENIAKSMAEGEVLQIVVFSVIFGIALIMVPEKKRKVMVDFTQSLSEVM 228 Query: 188 FNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICRAH 247 F N++M APIG AMA+T+G G+ L+ L +L++ Y ++FV++V I Sbjct: 229 FKFTNIVMYFAPIGVGAAMAYTVGHMGLSVLIPLLKLLLTLYGALLVFVIIVFIPIALFI 288 Query: 248 GFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDGT 307 + I+ I E + I T+SSE+ALPR + ME +G + +V V+P GYSFNLDGT Sbjct: 289 KLDLRAFIKAIGEPVSIAFATTSSEAALPRAMEAMESIGVPRKIVSFVMPMGYSFNLDGT 348 Query: 308 SIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHLP 367 ++YL++A+VF+AQA + I Q+ ++ L+++SKG AG+ + ++L T +A +LP Sbjct: 349 TLYLSLASVFVAQAAGIDLSIGEQLIMVFTLMVTSKGVAGIPRASLVILMGT-AASFNLP 407 Query: 368 VAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELD 408 V + +ILGID M AR N+VGN +A+ V+AKW E D Sbjct: 408 VWPIFIILGIDELMDMARTSINVVGNCLASAVIAKWEGEFD 448 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: 530 Number of extensions: 20 Number of successful extensions: 4 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: 470 Length adjustment: 33 Effective length of query: 411 Effective length of database: 437 Effective search space: 179607 Effective search space used: 179607 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 24 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