Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate H281DRAFT_01363 H281DRAFT_01363 aerobic C4-dicarboxylate transport protein
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Burk376:H281DRAFT_01363 Length = 433 Score = 479 bits (1232), Expect = e-140 Identities = 236/414 (57%), Positives = 316/414 (76%) Query: 4 RQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGI 63 ++P Y++LYF V AI IG+LLGHF P V +KPLGD FIKLIKMVI PIIFCTVV+GI Sbjct: 15 KKPFYRTLYFHVFAAIIIGVLLGHFAPSLAVKMKPLGDAFIKLIKMVIGPIIFCTVVTGI 74 Query: 64 AGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYV 123 AGM +MK VG+ GG ALLYFEIVST++L+IGLV ++ PG+G ++D +T+D +A Y Sbjct: 75 AGMGDMKKVGRVGGKALLYFEIVSTLSLVIGLVAGHIFHPGSGFNLDPATIDTKALAGYT 134 Query: 124 TAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRF 183 TA Q+ V F++++IP+T+ GAFA+G++LQ+L+ SV+FG AL G G+P++ ID F Sbjct: 135 TAAHQQNTVEFLMHIIPDTVTGAFASGNVLQILLISVLFGAALAATGERGRPLIAMIDYF 194 Query: 184 AHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAI 243 AH F I+++IMK+A IGA G++AFTIG YG+G++V L +L+ FY T +FV+VVLGAI Sbjct: 195 AHTFFGIVHIIMKVAAIGAFGSIAFTIGTYGIGAVVPLLKLIGAFYATLAVFVIVVLGAI 254 Query: 244 CRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFN 303 R GFS+ + + YIREE+LIVLGTSSSE+ALP+ML K+ERLG KSVVGLVIP GYSFN Sbjct: 255 SRLLGFSIFRFMSYIREEILIVLGTSSSEAALPQMLEKLERLGCSKSVVGLVIPAGYSFN 314 Query: 304 LDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAV 363 LDGT+IYLTMA +FIAQA + + +T Q+TL+ V +L+SKGA+GV G+ F++L +TL Sbjct: 315 LDGTNIYLTMAVLFIAQAFNIELSLTQQLTLVGVAMLTSKGASGVAGAAFVMLTSTLLVF 374 Query: 364 GHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELA 417 +PV+G+ LILGI RFM A+ N +GN VAT+VV+ W ELD +L A ++ Sbjct: 375 PLIPVSGMVLILGIHRFMGTGLAIANTIGNGVATLVVSAWEHELDRSKLNAGMS 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: 623 Number of extensions: 27 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: 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