Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate CCNA_00264 CCNA_00264 C4-dicarboxylate transport protein
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__Caulo:CCNA_00264 Length = 417 Score = 274 bits (701), Expect = 3e-78 Identities = 151/410 (36%), Positives = 245/410 (59%), Gaps = 16/410 (3%) Query: 7 KSLYFQVLTAIAIGILLG----HFYPEIG-----EQMKPLGDGFVKLIKMIIAPVIFCTV 57 K + ++ ++ +G+L+G F G + + + D F++LIKMIIAP++F T+ Sbjct: 3 KRFAYLIIASMILGVLVGWTCNQFLDPAGAKSAADNLSIITDIFLRLIKMIIAPLVFTTL 62 Query: 58 VTGIAGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAV 117 V G+A ME AVGR GA + +F S ++L++GL++V+++ PGAG+N+ + K Sbjct: 63 VAGVAHMEDAAAVGRIGAKTMTWFIGASAVSLVLGLLMVHLLDPGAGLNMAHVDVAMKTT 122 Query: 118 AVYADQAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNV 177 A D +G FI ++P S+ A A ILQ+++F++ G A+ L K I + Sbjct: 123 AT-TDAFTLKG---FITHLVPTSIFDAMAKNEILQIVVFSLFVGTAVAALDDKAPQILEL 178 Query: 178 IESFSQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITC-ILFVVL 236 +E +Q++ + +M+LAP+ F A+A TI G+G L G+ ++ FY +L+ +L Sbjct: 179 VEQAAQIMLKVTGFVMKLAPLAIFAALASTIATQGLGMLATYGKFVLGFYSAMGVLWALL 238 Query: 237 VLGSIAKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPT 296 + + G + IR+ +L+ T+SSE+A PR+LD + K+G R+ +V V+P Sbjct: 239 FIAGLL-VLGKRVIPLFGVIRDPVLLAFSTASSEAAYPRILDSLPKVGVRRRIVSFVLPL 297 Query: 297 GYSFNLDGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAA 356 GYSFNLDG+ +Y T A +FI QA ++ + QI +L++L+++SKG AGV + +V+ A Sbjct: 298 GYSFNLDGSMLYCTFATMFIVQAHGVELTVQQQIFMLLLLMVTSKGIAGVPRASLVVIMA 357 Query: 357 TLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELD 406 TL+ G LP A +AL+LG+D + R+ TN+VGN VA VVAKW ELD Sbjct: 358 TLTYFG-LPEAWIALVLGVDHLLDMGRSATNVVGNSVAAAVVAKWEGELD 406 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: 436 Number of extensions: 18 Number of successful extensions: 4 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: 417 Length adjustment: 32 Effective length of query: 396 Effective length of database: 385 Effective search space: 152460 Effective search space used: 152460 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: 50 (23.9 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