Align neutral amino acid transporter B(0) (characterized)
to candidate PfGW456L13_2016 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate, aspartate
Query= CharProtDB::CH_091706 (553 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2016 Length = 444 Score = 149 bits (377), Expect = 2e-40 Identities = 118/424 (27%), Positives = 208/424 (49%), Gaps = 52/424 (12%) Query: 92 GELLLRLLKMIILPLVVCSLIGGAASL-DPSALGRVGAWALLFFLVTTLLASALGVGLAL 150 G+ ++L+KM+I P++ C+++ G A + + ++G+ G +ALL+F + + LA +G+ + Sbjct: 40 GDGFIKLIKMVIAPIIFCTVVSGIAGMQNMKSVGKTGGYALLYFEIVSTLALLIGLVVVN 99 Query: 151 ALKPGAAVTAITSINDSVVDPCARSAPTKEALDSFLDLVRNIFPSNLVSAAFRSFATSYE 210 ++PGA + S D+ SA +++ +F V N+ P+ +V A FA Sbjct: 100 VVQPGAGMHIDVSTLDTSKIAGFISAGKDQSIIAF---VLNVIPNTIVGA----FANG-- 150 Query: 211 PKDNSCKIPQSCIQREINSTMVQLLCEVEGMNILGLVVFAIVFGVALRKLGPEGELLIRF 270 +IL +++F+++FG AL +LG G+ ++ F Sbjct: 151 -------------------------------DILQVLMFSVIFGFALHRLGAYGKPVLDF 179 Query: 271 FNSFNDATMVLVSWIMWYAPVGILFLVASKIVEMKDVRQLFISLGKYILCCLLGHAIHGL 330 + F +++ IM APVG +A I V L + LG+ ++C + + L Sbjct: 180 IDRFAHVMFNIINMIMKLAPVGAFGAMAFTIGAY-GVGSL-VQLGQLMICFYITCILFVL 237 Query: 331 LVLPLIYFLFTRKNPY---RFLWGIMTPLATAFGTSSSSATLPLMMKCVEEKNGVAKHIS 387 LVL I R + + + + I L GTSSS + LP M+ +E + G K + Sbjct: 238 LVLGAI----CRAHGFSVIKLIRYIREELLIVLGTSSSESALPRMLIKLE-RLGAQKSVV 292 Query: 388 RFILPIGATVNMDGAALFQCVAAVFIAQLNGVSLDFVKIITILVTATASSVGAAGIPAGG 447 ++P G + N+DG +++ +AAVFIAQ +D IT+L+ SS GAAG+ G Sbjct: 293 GLVIPTGYSFNLDGTSIYLTMAAVFIAQATDTPMDLTAQITLLLVLLLSSKGAAGVTGSG 352 Query: 448 VLTLAIILEAVS-LPVKDISLILAVDWLVDRSCTVLNVEGDAFGAGLLQSYVDRTKMPSS 506 + LA L AV LPV ++LIL +D + + + N+ G+A ++ +V + Sbjct: 353 FIVLAATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATLVVAKWVKELDEDTL 412 Query: 507 EPEL 510 + EL Sbjct: 413 QVEL 416 Lambda K H 0.323 0.138 0.406 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: 432 Number of extensions: 19 Number of successful extensions: 3 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: 553 Length of database: 444 Length adjustment: 34 Effective length of query: 519 Effective length of database: 410 Effective search space: 212790 Effective search space used: 212790 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 52 (24.6 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