Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate RR42_RS33745 RR42_RS33745 C4-dicarboxylate transporter
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__Cup4G11:RR42_RS33745 Length = 452 Score = 490 bits (1261), Expect = e-143 Identities = 237/415 (57%), Positives = 319/415 (76%) Query: 1 MKTSLFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTG 60 MK L SLY QVL A+A GILLG F P IG +KPLGD F++LIKM+ AP+IF TVV G Sbjct: 1 MKRRLISSLYVQVLIAVAAGILLGIFMPHIGSALKPLGDIFIRLIKMVFAPIIFATVVLG 60 Query: 61 IAGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVY 120 IA MESMK +GR G ALLYFE++ST AL++G+I+VNVVQPG GMNVDPATLD K++A Y Sbjct: 61 IAKMESMKDLGRVGWRALLYFEVLSTFALLLGVIVVNVVQPGHGMNVDPATLDTKSIAAY 120 Query: 121 ADQAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIES 180 Q K +GI+ F+++++P S++ A A +ILQ+L+F+V G AL LG +G+ ++S Sbjct: 121 TAQVKHEGIMDFLLNLVPMSIMDALAKNDILQILVFSVFMGVALAHLGERGKPFVAALDS 180 Query: 181 FSQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGS 240 F+ +F I+ MIMR+AP+ AFGAM+FT+GKYG G++ LG+L+ Y TC LFV++VLG+ Sbjct: 181 FANAMFAIVGMIMRVAPVAAFGAMSFTVGKYGFGSIASLGKLVATMYGTCALFVLIVLGA 240 Query: 241 IAKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSF 300 I + GF +F F++YI++E+L VLGTSSSES +P+++ K+E +G K VVGLV+P G +F Sbjct: 241 ICRICGFGLFNFLKYIKDEILTVLGTSSSESVIPQLMRKLENVGVSKPVVGLVVPAGLTF 300 Query: 301 NLDGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSA 360 N DG IY TMAA+FIAQATN+ + + Q +L VLLL+SKG+AG+TGSGFI LAATL++ Sbjct: 301 NPDGQCIYYTMAAIFIAQATNTPLTLTDQFVVLGVLLLTSKGSAGITGSGFITLAATLAS 360 Query: 361 VGHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLN 415 +G +PVAG+ L+LG+DRFMSEARA+TN +GN VAT+ +AKWV LD ++ VLN Sbjct: 361 LGKIPVAGMVLLLGVDRFMSEARAITNTIGNAVATMAIAKWVGALDEDRVQRVLN 415 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: 573 Number of extensions: 26 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: 452 Length adjustment: 32 Effective length of query: 396 Effective length of database: 420 Effective search space: 166320 Effective search space used: 166320 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