Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate RR42_RS33745 RR42_RS33745 C4-dicarboxylate transporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Cup4G11:RR42_RS33745 Length = 452 Score = 491 bits (1263), Expect = e-143 Identities = 248/437 (56%), Positives = 327/437 (74%), Gaps = 2/437 (0%) Query: 4 RQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGI 63 ++ L SLY QV++A+A GILLG F P G ALKPLGD FI+LIKMV APIIF TVV GI Sbjct: 2 KRRLISSLYVQVLIAVAAGILLGIFMPHIGSALKPLGDIFIRLIKMVFAPIIFATVVLGI 61 Query: 64 AGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYV 123 A M++MK +G+ G ALLYFE++ST ALL+G++VVNVVQPG+GM++D +TLD +AAY Sbjct: 62 AKMESMKDLGRVGWRALLYFEVLSTFALLLGVIVVNVVQPGHGMNVDPATLDTKSIAAYT 121 Query: 124 TAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRF 183 K + I+ F+LN++P +I+ A A DILQ+L+FSV G AL LG GKP + +D F Sbjct: 122 AQVKHEGIMDFLLNLVPMSIMDALAKNDILQILVFSVFMGVALAHLGERGKPFVAALDSF 181 Query: 184 AHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAI 243 A+ MF I+ MIM++AP+ A GAM+FT+G YG GS+ LG+L+ Y TC LFVL+VLGAI Sbjct: 182 ANAMFAIVGMIMRVAPVAAFGAMSFTVGKYGFGSIASLGKLVATMYGTCALFVLIVLGAI 241 Query: 244 CRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFN 303 CR GF + ++YI++E+L VLGTSSSES +P+++ K+E +G K VVGLV+P G +FN Sbjct: 242 CRICGFGLFNFLKYIKDEILTVLGTSSSESVIPQLMRKLENVGVSKPVVGLVVPAGLTFN 301 Query: 304 LDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAV 363 DG IY TMAA+FIAQAT+T + +T Q +L VLLL+SKG+AG+TGSGFI LAATL+++ Sbjct: 302 PDGQCIYYTMAAIFIAQATNTPLTLTDQFVVLGVLLLTSKGSAGITGSGFITLAATLASL 361 Query: 364 GHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGGRAI 423 G +PVAG+ L+LG+DRFMSEARA+TN +GNAVAT+ +AKWV LDED++Q L G Sbjct: 362 GKIPVAGMVLLLGVDRFMSEARAITNTIGNAVATMAIAKWVGALDEDRVQRVL--NGEVD 419 Query: 424 SDTREEDDLGVAEGPTP 440 + E+ GVA P P Sbjct: 420 PEDLEQLYEGVAPEPIP 436 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: 586 Number of extensions: 22 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: 452 Length adjustment: 33 Effective length of query: 411 Effective length of database: 419 Effective search space: 172209 Effective search space used: 172209 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