Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate PfGW456L13_2016 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate, aspartate
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2016 Length = 444 Score = 624 bits (1610), Expect = 0.0 Identities = 312/406 (76%), Positives = 368/406 (90%) Query: 5 LFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGM 64 L+KSLYFQV+ AIAIGILLGHFYP+ G +KPLGDGF+KLIKM+IAP+IFCTVV+GIAGM Sbjct: 7 LYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGM 66 Query: 65 ESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQA 124 ++MK+VG+TG ALLYFEIVST+AL+IGL++VNVVQPGAGM++D +TLD +A + Sbjct: 67 QNMKSVGKTGGYALLYFEIVSTLALLIGLVVVNVVQPGAGMHIDVSTLDTSKIAGFISAG 126 Query: 125 KDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQV 184 KDQ I+AF+++VIP +++GAFA+G+ILQVL+F+V+FGFALHRLG+ G+ + + I+ F+ V Sbjct: 127 KDQSIIAFVLNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHV 186 Query: 185 IFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKA 244 +F IINMIM+LAP+GAFGAMAFTIG YGVG+LVQLGQL+ICFYITCILFV+LVLG+I +A Sbjct: 187 MFNIINMIMKLAPVGAFGAMAFTIGAYGVGSLVQLGQLMICFYITCILFVLLVLGAICRA 246 Query: 245 TGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDG 304 GFS+ K IRYIREELLIVLGTSSSESALPRML K+E+LG +KSVVGLVIPTGYSFNLDG Sbjct: 247 HGFSVIKLIRYIREELLIVLGTSSSESALPRMLIKLERLGAQKSVVGLVIPTGYSFNLDG 306 Query: 305 TSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 364 TSIYLTMAAVFIAQAT++ MD+ QITLL+VLLLSSKGAAGVTGSGFIVLAATLSAVGHL Sbjct: 307 TSIYLTMAAVFIAQATDTPMDLTAQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 366 Query: 365 PVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKL 410 PVAGLALILGIDRFMSEARALTNLVGN VAT+VVAKWVKELD L Sbjct: 367 PVAGLALILGIDRFMSEARALTNLVGNAVATLVVAKWVKELDEDTL 412 Lambda K H 0.327 0.142 0.401 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: 687 Number of extensions: 20 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: 428 Length of database: 444 Length adjustment: 32 Effective length of query: 396 Effective length of database: 412 Effective search space: 163152 Effective search space used: 163152 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 (21.7 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