Align 2-oxoacid:ferredoxin oxidoreductase 1, subunit beta; OFOR1; EC 1.2.7.11 (characterized)
to candidate Ga0059261_0324 Ga0059261_0324 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit
Query= SwissProt::Q9YA11 (318 letters) >FitnessBrowser__Korea:Ga0059261_0324 Length = 343 Score = 191 bits (484), Expect = 3e-53 Identities = 95/196 (48%), Positives = 125/196 (63%), Gaps = 1/196 (0%) Query: 17 WCPGCGDFGILAAMQKAFAELNLDPAQTVVVSGIGCSSKTPHFINVNGVHTIHGRGIAFA 76 WCPGCGD+ IL A+Q+ E+ P TV +SGIGCSS+ P+++ G HTIHGR A A Sbjct: 23 WCPGCGDYAILKAVQRTMPEIGATPENTVFISGIGCSSRFPYYMETYGFHTIHGRAPAVA 82 Query: 77 TGIKLANPQLKVIVNGGDGDLLGIGVAHFVALGRRNLDVTVLIHNNKVYGLTKGQASPTL 136 TG+KLANP L V + GDGD L IG H + L RRNL+ VL+ NN++YGLTKGQ SPT Sbjct: 83 TGVKLANPDLDVWIITGDGDGLSIGGNHTMHLLRRNLNCQVLLFNNEIYGLTKGQYSPTS 142 Query: 137 RRGEKVKSLPVPNLQDAVNPIALAIASGYTFVARAYSLWVDHLKEILKAAINHKGSAVID 196 R G + S P ++ P A A+ SG F+AR + +L +LKAA H+G+A ++ Sbjct: 143 REGTRSPSTPFGSVDHPAKPCAYALGSGARFIARGIDVH-KNLPSVLKAAHAHQGAAFVE 201 Query: 197 VLQPCVTYNDIYTAEF 212 + Q C+ YND A F Sbjct: 202 IFQNCIVYNDDVFAPF 217 Lambda K H 0.319 0.137 0.416 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: 307 Number of extensions: 15 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: 318 Length of database: 343 Length adjustment: 28 Effective length of query: 290 Effective length of database: 315 Effective search space: 91350 Effective search space used: 91350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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