Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate GFF1853 PS417_09425 C4-dicarboxylate transporter
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__WCS417:GFF1853 Length = 437 Score = 471 bits (1213), Expect = e-137 Identities = 234/425 (55%), Positives = 316/425 (74%), Gaps = 1/425 (0%) Query: 5 LFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGM 64 L +LY QVL AIA+G+L+GH +P+IG +KPLGDGF+KLIKMII P+IFCTVV+GI M Sbjct: 6 LLGTLYIQVLIAIALGVLIGHQWPQIGIDLKPLGDGFIKLIKMIIGPIIFCTVVSGITSM 65 Query: 65 ESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQA 124 +K VGR G ALLYFE+VSTIAL+IG++ +++ PG G N+D TLD+ A+A + QA Sbjct: 66 HDVKQVGRVGGKALLYFEVVSTIALLIGILAAHLLHPGVGFNIDVKTLDSSAIAGFVGQA 125 Query: 125 KD-QGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQ 183 + +GI F++ VIPA+ AF+ G IL VL +VLFG L +G KG+ + VI S+ Sbjct: 126 EHGEGITGFLLHVIPATFFDAFSKGEILPVLFVSVLFGVGLVMVGEKGRPLVGVINQASE 185 Query: 184 VIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAK 243 V F I+ +I R+APIGAFGA+AFTIGKYGVG+L+ L +L+ FY+T F+ +VLGSIA+ Sbjct: 186 VFFRIVGIISRVAPIGAFGAIAFTIGKYGVGSLLPLLKLVGTFYVTAFFFIAVVLGSIAR 245 Query: 244 ATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLD 303 GFSIFK + YI+ ELLIVLGTSSSESALP+++ K+E LG K VVG+V+PTGY+FNLD Sbjct: 246 YAGFSIFKLMGYIKSELLIVLGTSSSESALPQLIQKLESLGASKGVVGIVVPTGYTFNLD 305 Query: 304 GTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGH 363 GT+IY+T+A +F+AQATN + + Q+TLL V +L+SKGA V G+GF+ LAA+L+ V Sbjct: 306 GTNIYMTLAVLFLAQATNIHLPLEQQLTLLAVAMLTSKGAGAVVGAGFVALAASLAVVPT 365 Query: 364 LPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRAPDGKT 423 +PVA + LILG+DRFM+E R+LTN++GN VA +VVA W ELD +K+ + R + Sbjct: 366 VPVAAMVLILGVDRFMAECRSLTNIIGNAVAALVVAAWEGELDREKMAPIALKRGRHARA 425 Query: 424 HELSS 428 E ++ Sbjct: 426 AEAAA 430 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: 611 Number of extensions: 24 Number of successful extensions: 2 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: 437 Length adjustment: 32 Effective length of query: 396 Effective length of database: 405 Effective search space: 160380 Effective search space used: 160380 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