Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate PP_1188 PP_1188 C4-dicarboxylate transport protein
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Putida:PP_1188 Length = 440 Score = 761 bits (1964), Expect = 0.0 Identities = 392/438 (89%), Positives = 413/438 (94%) Query: 1 MTTRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVV 60 MTTRQPLYKSLY QV+VAI IGILLGH+YP+TGVALKPLGDGF+KLIKMVIAPIIFCTVV Sbjct: 1 MTTRQPLYKSLYVQVLVAITIGILLGHYYPETGVALKPLGDGFVKLIKMVIAPIIFCTVV 60 Query: 61 SGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVA 120 SGIAGMQ+MKSVGKTGGYALLYFEIVSTIAL+IGLVVVNVV+PG GMHIDVSTL+AS VA Sbjct: 61 SGIAGMQSMKSVGKTGGYALLYFEIVSTIALIIGLVVVNVVKPGAGMHIDVSTLNASSVA 120 Query: 121 AYVTAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFI 180 AY AG Q+ VGF+LNVIPNT+VGAFANGDILQVLMFSV+FGFALHRLG+YGKPVLD I Sbjct: 121 AYAAAGAQQTTVGFLLNVIPNTVVGAFANGDILQVLMFSVLFGFALHRLGSYGKPVLDMI 180 Query: 181 DRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVL 240 DRFAHVMFNIINMIMKLAPIGA GAMAFTIG YGVGSLVQLG LM CFYITC+LFVLVVL Sbjct: 181 DRFAHVMFNIINMIMKLAPIGAFGAMAFTIGQYGVGSLVQLGYLMACFYITCLLFVLVVL 240 Query: 241 GAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGY 300 G ICRAHGFSV+KLIRYIREELLIVLGTSSSESALPRML KMERLGAKKSVVGLVIPTGY Sbjct: 241 GGICRAHGFSVIKLIRYIREELLIVLGTSSSESALPRMLAKMERLGAKKSVVGLVIPTGY 300 Query: 301 SFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATL 360 SFNLDGTSIYLTMAAVFIAQATDT MDITHQITLLLVLL++SKGAAGVTGSGFIVLAATL Sbjct: 301 SFNLDGTSIYLTMAAVFIAQATDTTMDITHQITLLLVLLVASKGAAGVTGSGFIVLAATL 360 Query: 361 SAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGG 420 SAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKE+D D+L +EL SGG Sbjct: 361 SAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKEMDNDKLASELDSGG 420 Query: 421 RAISDTREEDDLGVAEGP 438 + DTR DDLGVAEGP Sbjct: 421 APLIDTRPTDDLGVAEGP 438 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: 764 Number of extensions: 24 Number of successful extensions: 1 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: 440 Length adjustment: 32 Effective length of query: 412 Effective length of database: 408 Effective search space: 168096 Effective search space used: 168096 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