Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate Ac3H11_1083 C4-dicarboxylate transport protein
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1083 Length = 443 Score = 424 bits (1091), Expect = e-123 Identities = 207/414 (50%), Positives = 297/414 (71%), Gaps = 3/414 (0%) Query: 8 SLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMESM 67 SL+ +V+ A+ G+ +G +P+ Q+KPLGDGF+KLIKM+I ++FC VV GIAG + Sbjct: 7 SLFGRVILALIAGVAIGLLWPDTAVQLKPLGDGFIKLIKMLIPLIVFCVVVHGIAGTGDL 66 Query: 68 KAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKDQ 127 K VGR G +L+YFE+V+TIAL++GL + +PG GMNVDP LD KA+ YAD A Sbjct: 67 KRVGRVGIKSLIYFEVVTTIALVLGLALAFWFEPGVGMNVDPKALDPKAMGAYADNASKL 126 Query: 128 ---GIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQV 184 G F++ +IP + + AFA+G++LQVLLF+++FG AL +G +G + +IE S V Sbjct: 127 TGGGFSDFLLKLIPTTAVSAFANGDVLQVLLFSIVFGCALALMGDRGARVTGLIEDLSHV 186 Query: 185 IFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKA 244 +F + +I++LAP+G GA+AFT+GKYG+G+L QLG L++ FY +FVV+VLG I + Sbjct: 187 LFKTMGLIIKLAPLGVLGAIAFTVGKYGIGSLKQLGMLVVLFYAAVFIFVVVVLGLIMRV 246 Query: 245 TGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDG 304 +GFS+FK +RY+REEL +V T+SS+S LP+++ K++ +G R S VGLVIPTGYSFNLD Sbjct: 247 SGFSLFKLLRYLREELAVVFATTSSDSVLPQIMAKLKHMGIRDSTVGLVIPTGYSFNLDA 306 Query: 305 TSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 364 SIY+T+AAVFIAQATN+ + + +T+L + L++SKGA GV GS +VLAATL A+ + Sbjct: 307 FSIYITLAAVFIAQATNTPITMTDLLTILAISLVTSKGAHGVPGSAIVVLAATLHAIPAI 366 Query: 365 PVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRA 418 P GL L+L +D FM ARAL NL+GN VAT+ +A W ++D + VL+ ++ Sbjct: 367 PAIGLVLVLSVDWFMGIARALGNLIGNCVATVAIAAWEGDIDRDRAHAVLDGQS 420 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: 585 Number of extensions: 33 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: 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