Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate Ac3H11_1083 C4-dicarboxylate transport protein
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1083 Length = 443 Score = 420 bits (1080), Expect = e-122 Identities = 214/410 (52%), Positives = 292/410 (71%), Gaps = 3/410 (0%) Query: 10 SLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQNM 69 SL+ +VI+A+ G+ +G +P T V LKPLGDGFIKLIKM+I I+FC VV GIAG ++ Sbjct: 7 SLFGRVILALIAGVAIGLLWPDTAVQLKPLGDGFIKLIKMLIPLIVFCVVVHGIAGTGDL 66 Query: 70 KSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAGKDQ 129 K VG+ G +L+YFE+V+TIAL++GL + +PG GM++D LD + AY Sbjct: 67 KRVGRVGIKSLIYFEVVTTIALVLGLALAFWFEPGVGMNVDPKALDPKAMGAYADNASKL 126 Query: 130 SIVGF---ILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHV 186 + GF +L +IP T V AFANGD+LQVL+FS++FG AL +G G V I+ +HV Sbjct: 127 TGGGFSDFLLKLIPTTAVSAFANGDVLQVLLFSIVFGCALALMGDRGARVTGLIEDLSHV 186 Query: 187 MFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICRA 246 +F + +I+KLAP+G LGA+AFT+G YG+GSL QLG L++ FY +FV+VVLG I R Sbjct: 187 LFKTMGLIIKLAPLGVLGAIAFTVGKYGIGSLKQLGMLVVLFYAAVFIFVVVVLGLIMRV 246 Query: 247 HGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDG 306 GFS+ KL+RY+REEL +V T+SS+S LP+++ K++ +G + S VGLVIPTGYSFNLD Sbjct: 247 SGFSLFKLLRYLREELAVVFATTSSDSVLPQIMAKLKHMGIRDSTVGLVIPTGYSFNLDA 306 Query: 307 TSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 366 SIY+T+AAVFIAQAT+T + +T +T+L + L++SKGA GV GS +VLAATL A+ + Sbjct: 307 FSIYITLAAVFIAQATNTPITMTDLLTILAISLVTSKGAHGVPGSAIVVLAATLHAIPAI 366 Query: 367 PVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAEL 416 P GL L+L +D FM ARAL NL+GN VATV +A W ++D D+ A L Sbjct: 367 PAIGLVLVLSVDWFMGIARALGNLIGNCVATVAIAAWEGDIDRDRAHAVL 416 Lambda K H 0.326 0.142 0.402 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: 609 Number of extensions: 22 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: 444 Length of database: 443 Length adjustment: 32 Effective length of query: 412 Effective length of database: 411 Effective search space: 169332 Effective search space used: 169332 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 (21.6 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