Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate GFF4198 PS417_21500 C4-dicarboxylate transporter
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__WCS417:GFF4198 Length = 443 Score = 632 bits (1630), Expect = 0.0 Identities = 320/410 (78%), Positives = 367/410 (89%) Query: 5 LFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGM 64 ++KSLYFQV+ AI IGILLGHFYP+ G +KPLGDGF+KLIKM+IAP+IFCTVV+GIAGM Sbjct: 7 IYKSLYFQVIVAIVIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGM 66 Query: 65 ESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQA 124 +SMK+VG+TG ALLYFEIVST+AL+IGLI+VNVVQPG GM++D ATLDA VA Y Sbjct: 67 QSMKSVGKTGGYALLYFEIVSTVALLIGLIVVNVVQPGNGMHIDVATLDASKVAAYVTAG 126 Query: 125 KDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQV 184 KDQ IV FI++VIP +++GAFA+G+ILQVL+F+V+FGFALHRLG+ G+ + + I+ F+ V Sbjct: 127 KDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHV 186 Query: 185 IFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKA 244 +F IINMIM+LAPIGA GAMAFTIG YGVG+LVQLGQL+ICFYITC+LFV++VLG I +A Sbjct: 187 MFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCLLFVLVVLGGICRA 246 Query: 245 TGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDG 304 GFS+ K IRYIREELLIVLGTSSSESALPRML KME+LG +KSVVGLVIPTGYSFNLDG Sbjct: 247 HGFSVIKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDG 306 Query: 305 TSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 364 TSIYLTMAAVFIAQAT++ MDI HQITLL+VLLLSSKGAAGVTGSGFIVLAATLSAVGHL Sbjct: 307 TSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 366 Query: 365 PVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVL 414 PVAGLALILGIDRFMSEARALTNLVGN VATIVVAKWVKELD KL L Sbjct: 367 PVAGLALILGIDRFMSEARALTNLVGNAVATIVVAKWVKELDTDKLQSEL 416 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: 703 Number of extensions: 21 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: 443 Length adjustment: 32 Effective length of query: 396 Effective length of database: 411 Effective search space: 162756 Effective search space used: 162756 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