Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate PP_2255 PP_2255 C4-dicarboxylate transport protein
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Putida:PP_2255 Length = 436 Score = 403 bits (1036), Expect = e-117 Identities = 204/406 (50%), Positives = 289/406 (71%), Gaps = 1/406 (0%) Query: 9 KSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQN 68 +S++ QV++ +A+GI G +P + LKPLGDGFIKLIKM+I I+FC VVSGI+G + Sbjct: 7 RSIFLQVVLGLALGIACGLSFPDLSLQLKPLGDGFIKLIKMLIGLIVFCVVVSGISGAGD 66 Query: 69 MKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAGKD 128 +K VG+ G +++YFE+++T+AL+IGLV G+G +I + L A+ G+ Sbjct: 67 LKKVGRIGLKSVIYFEVLTTLALVIGLVFAFTSGIGSGANIHLDQLSAADANGLAERGQH 126 Query: 129 -QSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHVM 187 F +++IP +++GAFA+ +ILQVL+FSV+FG AL+ +G + I+ +HV+ Sbjct: 127 IHGATAFFMDLIPTSVIGAFADNNILQVLLFSVLFGSALNLVGDSAAGISRLINELSHVI 186 Query: 188 FNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICRAH 247 F I+ MI++LAPIG GA+AFT YG+ SL LG L+ FY+TC FVL+VLG + R Sbjct: 187 FRIMGMIVRLAPIGVFGAIAFTTSKYGLASLQHLGGLVALFYLTCAGFVLIVLGTVMRLS 246 Query: 248 GFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDGT 307 G +L LI+Y+REEL IVLGT+SS++ LP+++ K+E LG S VGLVIPTGYSFNLDG Sbjct: 247 GLKLLPLIKYLREELTIVLGTASSDAVLPQIMRKLEHLGIGSSTVGLVIPTGYSFNLDGF 306 Query: 308 SIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHLP 367 SIYLT+A VFIA AT T +++T +T+LLV L++SKGA G+ GS ++LAATL+AV +P Sbjct: 307 SIYLTLAIVFIANATGTPLEMTDLLTILLVSLVTSKGAHGIPGSALVILAATLTAVPAIP 366 Query: 368 VAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQ 413 V GL L+L +D FM RALTNL+GN VATV +A+W K++D ++ Q Sbjct: 367 VVGLVLVLAVDWFMGIGRALTNLIGNCVATVAIARWEKDIDLERAQ 412 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: 574 Number of extensions: 28 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: 436 Length adjustment: 32 Effective length of query: 412 Effective length of database: 404 Effective search space: 166448 Effective search space used: 166448 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