Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate GFF1853 PS417_09425 C4-dicarboxylate transporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__WCS417:GFF1853 Length = 437 Score = 471 bits (1213), Expect = e-137 Identities = 238/422 (56%), Positives = 321/422 (76%), Gaps = 2/422 (0%) Query: 1 MTTRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVV 60 MT R+ L +LY QV++AIA+G+L+GH +PQ G+ LKPLGDGFIKLIKM+I PIIFCTVV Sbjct: 1 MTIRK-LLGTLYIQVLIAIALGVLIGHQWPQIGIDLKPLGDGFIKLIKMIIGPIIFCTVV 59 Query: 61 SGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVA 120 SGI M ++K VG+ GG ALLYFE+VSTIALLIG++ +++ PG G +IDV TLD+S +A Sbjct: 60 SGITSMHDVKQVGRVGGKALLYFEVVSTIALLIGILAAHLLHPGVGFNIDVKTLDSSAIA 119 Query: 121 AYV-TAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDF 179 +V A + I GF+L+VIP T AF+ G+IL VL SV+FG L +G G+P++ Sbjct: 120 GFVGQAEHGEGITGFLLHVIPATFFDAFSKGEILPVLFVSVLFGVGLVMVGEKGRPLVGV 179 Query: 180 IDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVV 239 I++ + V F I+ +I ++APIGA GA+AFTIG YGVGSL+ L +L+ FY+T F+ VV Sbjct: 180 INQASEVFFRIVGIISRVAPIGAFGAIAFTIGKYGVGSLLPLLKLVGTFYVTAFFFIAVV 239 Query: 240 LGAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTG 299 LG+I R GFS+ KL+ YI+ ELLIVLGTSSSESALP+++ K+E LGA K VVG+V+PTG Sbjct: 240 LGSIARYAGFSIFKLMGYIKSELLIVLGTSSSESALPQLIQKLESLGASKGVVGIVVPTG 299 Query: 300 YSFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAAT 359 Y+FNLDGT+IY+T+A +F+AQAT+ H+ + Q+TLL V +L+SKGA V G+GF+ LAA+ Sbjct: 300 YTFNLDGTNIYMTLAVLFLAQATNIHLPLEQQLTLLAVAMLTSKGAGAVVGAGFVALAAS 359 Query: 360 LSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASG 419 L+ V +PVA + LILG+DRFM+E R+LTN++GNAVA +VVA W ELD +++ Sbjct: 360 LAVVPTVPVAAMVLILGVDRFMAECRSLTNIIGNAVAALVVAAWEGELDREKMAPIALKR 419 Query: 420 GR 421 GR Sbjct: 420 GR 421 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: 633 Number of extensions: 20 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: 437 Length adjustment: 32 Effective length of query: 412 Effective length of database: 405 Effective search space: 166860 Effective search space used: 166860 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